From d0344ec2304e2c4ef8f261b884e4e21d4e491c69 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Thu, 5 Dec 2024 12:54:27 -0600 Subject: [PATCH] Release Candidate 2024-12-05 --- obi.owl | 3913 +++++++++++++++++++-------------------- views/NIAID-GSC-BRC.owl | 185 +- views/obi-base.owl | 3416 +++++++++++++++------------------- views/obi.obo | 444 ++++- views/obi_core.owl | 124 +- 5 files changed, 3927 insertions(+), 4155 deletions(-) diff --git a/obi.owl b/obi.owl index 6469e90e..bc9dd2b1 100755 --- a/obi.owl +++ b/obi.owl @@ -13,7 +13,7 @@ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + en Ontology for Biomedical Investigations Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester @@ -80,7 +80,7 @@ http://creativecommons.org/licenses/by/4.0/ Ontology for Biomedical Investigations Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2024-10-25 + 2024-12-05 @@ -897,6 +897,19 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + + + + A serial number such as "12324X"; a stop sign; a written proper name such as "OBI + An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. + + + 2024-03-25 + has symbol + + + + @@ -1219,6 +1232,19 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + + + + disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C41009"^^xsd:string + An annotation property that links an ontology entity or a statement to a prefixed identifier or URI. + + + 2024-03-18 + has cross-reference + + + + @@ -12310,7 +12336,7 @@ editor = PRS specimen role liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient. - a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation + A role borne by a material entity that is obtained during a specimen collection process and that can be realized by performing measurements or observations on the specimen. 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. blood taken from animal: animal continues in study, whereas blood has role specimen. @@ -15323,6 +15349,7 @@ Proposal is to obsolete. + @@ -19941,25 +19968,30 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - urine specimen a portion of urine collected from an organism @@ -20044,25 +20076,30 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - blood specimen blood drawn from a human for glucose assay @@ -20143,9 +20180,10 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 specimen collection process - drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation + drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation, collecting a stone from a site - A planned process with the objective of collecting a specimen. + A planned process with the objective to obtain a material entity for potential use as an input upon which measurements or observations are performed. + Definition updated following discussion on 2024-10-07 OBI dev call. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. Philly2013: The specimen_role for the specimen is created during the specimen collection process. @@ -20456,10 +20494,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - - - - + @@ -20469,12 +20504,6 @@ http://sourceforge.net/p/obi/obi-terms/716/ - - - - - - sample from organism a material obtained from an organism in order to be a representative of the whole @@ -20601,23 +20630,6 @@ http://sourceforge.net/p/obi/obi-terms/716/ - - - - - - - - - - - - - - - - - @@ -20670,7 +20682,8 @@ http://sourceforge.net/p/obi/obi-terms/716/ specimen collection objective The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. - A objective specification to obtain a material entity for potential use as an input during an investigation. + A objective specification that is fulfilled by obtaining a material entity for potential use as an input upon which measurements or observations are performed. + OBI recommends against subclassing this term in order to avoid further parallel hierarchies between this term and specimen collection process. Bjoern Peters Bjoern Peters specimen collection objective @@ -21896,7 +21909,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + @@ -22631,7 +22644,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + @@ -22645,9 +22658,9 @@ the role 'adjuvant role' inheres in some 'material entity' a A material entity that has the material sample role OBI: workshop + sample sample population - - sample + https://github.com/obi-ontology/obi/issues/1013 material sample @@ -23769,7 +23782,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -24813,6 +24826,7 @@ placeholder + @@ -24898,39 +24912,43 @@ placeholder - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - pre-mortem specimen material obtained through a liver biopsy from a human patient a specimen that was taken from a live organism Bjoern Peters - MO_705 premortem + MO_705 premortem pre-mortem specimen @@ -25088,8 +25106,7 @@ placeholder Cytoplasmic RNA extraction from mammalian tissues to create cDNA library (Carninci P, Nakamura M, Sato K, Hayashizaki Y, Brownstein MJ. Cytoplasmic RNA extraction from fresh and frozen mammalian tissues. Biotechniques. 2002;33:306–309.) A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted. - PERSON: Chris Stoeckert - PERSON: Jie Zheng + PERSON:Chris Stoeckert UPenn Group cytoplasmic RNA extract @@ -25520,7 +25537,7 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. total RNA extract - Extraction of total RNA from cells with Qiagen mini RNeasy kit. + Extraction of total RNA from cells with Qiagen mini RNeasy kit A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen. PERSON: Chris Stoeckert @@ -25617,30 +25634,35 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + post mortem specimen @@ -25648,7 +25670,7 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. a specimen that was taken from a dead organism Bjoern Peters - MO_416 postmortem + MO_416 postmortem post mortem specimen @@ -25819,10 +25841,10 @@ Dev call Nov 22, 2010: To reflect this, the term's label has been updated t - - + + @@ -25838,23 +25860,17 @@ Dev call Nov 22, 2010: To reflect this, the term's label has been updated t - - + + - - - - - - - + + labeled DNA extract a labeled specimen that is the output of a labeling process and has grain labeled DNA to be able to detect DNA in future experiments. - Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. -Added duirng Mar 1, 2010 dev call + Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call Group: OBI group Group: OBI group labeled DNA extract @@ -25865,19 +25881,34 @@ Added duirng Mar 1, 2010 dev call - - - - - - - - cloacal specimen + + + + + + + + + + + + + + + + + + + + + + + + + cell specimen type of sample used in the PCIRN influenza network - A specimen obtained by inserting a swab deeply into the vent of the cloaca of -an organism and vigorously swabbing the wall. The swab should be deeply -stained with fecal material and is then placed in transport medium. + A specimen obtained by inserting a swab deeply into the vent of the cloaca of an organism and vigorously swabbing the wall. The swab should be deeply stained with fecal material and is then placed in transport medium. PERSON: Melanie Courtot WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf cloacal specimen @@ -26071,18 +26102,31 @@ stained with fecal material and is then placed in transport medium. - + + + + + + + + + + + + + + + - - + + nasopharyngeal aspirate specimen type of sample used in the PCIRN influenza network - A speciemn which derives from nasopharyngeal mucosa after -aspiration. + A specimen which derives from nasopharyngeal mucosa after aspiration. PERSON: Melanie Courtot WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf nasopharyngeal aspirate specimen @@ -26208,24 +26252,37 @@ Updated both textual and logical definition. Both input and output material of f + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - nasal swab specimen type of sample used in the PCIRN influenza network - A specimen obtained using a cotton swab on a stick, passed up the nostril to obtain a sample of -exudate and epithelial debris for microbiological or cellular examination. + A specimen obtained using a cotton swab on a stick, passed up the nostril to obtain a sample of exudate and epithelial debris for microbiological or cellular examination. PERSON: Melanie Courtot WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf nasal swab specimen @@ -26345,10 +26402,10 @@ exudate and epithelial debris for microbiological or cellular examination. - - + + @@ -26364,23 +26421,17 @@ exudate and epithelial debris for microbiological or cellular examination. - - + + - - - - - - - + + labeled RNA extract a labeled specimen that is the output of a labeling process and has grain labeled RNA to be able to detect RNA in future experiments. - Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. -Added duirng Mar 1, 2010 dev call + Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call Group: OBI group Group: OBI group labeled RNA extract @@ -26394,6 +26445,7 @@ Added duirng Mar 1, 2010 dev call + @@ -26413,18 +26465,10 @@ Added duirng Mar 1, 2010 dev call - - - - - - - - frozen specimen Frozen blood plasma @@ -27124,6 +27168,7 @@ Biochimie. 2010 Feb 18. + @@ -27143,17 +27188,10 @@ Biochimie. 2010 Feb 18. - - - - - - - paraffin specimen liver tissue embedded in paraffin @@ -27244,21 +27282,24 @@ Biochimie. 2010 Feb 18. - + + + + + + processed specimen - A tissue sample that has been sliced and stained for a histology study. -A blood specimen that has been centrifuged to obtain the white blood cells. A specimen that has been intentionally physically modified. + A tissue sample that has been sliced and stained for a histology study. Bjoern Peters Bjoern Peters - A tissue sample that has been sliced and stained for a histology study. processed specimen @@ -27484,6 +27525,7 @@ A blood specimen that has been centrifuged to obtain the white blood cells. + @@ -27503,16 +27545,10 @@ A blood specimen that has been centrifuged to obtain the white blood cells. - - - - - - lyophilized specimen freezing dried DNA @@ -27688,7 +27724,6 @@ In the examples above, a reagent is an operational component of a device, but th - fresh specimen a liver freshly removed from a rat @@ -27898,25 +27933,30 @@ In the examples above, a reagent is an operational component of a device, but th - - - - - - - - - + + + + + + + + + - - + + + + + + + - - - - - - + + + + + + agar stab specimen @@ -28658,167 +28698,152 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + + + + + + + nucleic acid extract + + An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. + Person: Jie Zheng + UPenn Group + nucleic acid extract + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ENU structure mapping assay + PMID:7002606 and PMID:2446263 + + A single-nucleotide-resolution nucleic acid structure mapping assay that determines the secondary structure of a nucleic acid at the nucleotide resolution scale which uses ENU as reagent and chemical probe + Philippe Rocca-Serra + single nucleotide resolution mapping assay using ENU probe + RNA ontology + ENU structure mapping assay + + + + + + + + - - + + + + + + + + + + + + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - nucleic acid extract - - An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. - PERSON: Jie Zheng - UPenn Group - nucleic acid extract + RNASE V1 structure mapping assay + PMID:7031604 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse V1 as reagent and enzymatic probe + Philippe Rocca-Serra + single nucleotide resolution mapping assay using RNAse V1 + RNA ontology + RNASE V1 structure mapping assay - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ENU structure mapping assay - PMID:7002606 and PMID:2446263 - - A single-nucleotide-resolution nucleic acid structure mapping assay that determines the secondary structure of a nucleic acid at the nucleotide resolution scale which uses ENU as reagent and chemical probe - Philippe Rocca-Serra - single nucleotide resolution mapping assay using ENU probe - RNA ontology - ENU structure mapping assay - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - RNASE V1 structure mapping assay - PMID:7031604 - - A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse V1 as reagent and enzymatic probe - Philippe Rocca-Serra - single nucleotide resolution mapping assay using RNAse V1 - RNA ontology - RNASE V1 structure mapping assay - - - - - - - + @@ -32185,10 +32210,10 @@ JZ: based on textual definition of edited document, it can be defined as N&S - - + + @@ -32204,25 +32229,19 @@ JZ: based on textual definition of edited document, it can be defined as N&S - - + + - - - - - - - + + labeled nucleic acid extract a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments. Person: Jie Zheng labeled extract MO_221 labeledExtract - labeled extract labeled nucleic acid extract @@ -42740,26 +42759,25 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - - - - - - - - - - - - - cell specimen + + + + + + + + + + + + + cell specimen A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture. - Discussed on obi call Jan 23, 2017. To improve cell specimen that include single cell specimen. Details see tracker: https://sourceforge.net/p/obi/obi-terms/828/ + Discussed on obi call Jan 23, 2017. To improve cell specimen that include single cell specimen. Details see tracker: https://sourceforge.net/p/obi/obi-terms/828 PERSON: Chris Stoeckert, Jie Zheng, Alexander Diehl MO_612 cell - cell specimen + cell specimen @@ -42839,27 +42857,32 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - + + - - - - - - - + + + + + + + + + + + + - + - specimen with known storage state + specimen with known storage state A specimen for which it is known whether it has been subjected to storage of a specified type. PERSON: Chris Stoeckert, Jie Zheng MO_95 BiosourceType - specimen with known storage state + specimen with known storage state @@ -43116,18 +43139,26 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html + - - - - - + - - - - + + + + + + + + + + + + + + + @@ -43135,13 +43166,13 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - specimen from organism + specimen from organism A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm). PERSON: Chris Stoeckert, Jie Zheng - tissue specimen + tissue specimen MO_954 organism_part - specimen from organism + specimen from organism @@ -44072,46 +44103,51 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - specimen with pre- or post-mortem status + + specimen with pre- or post-mortem status A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism. organizational term, used in description of specimen that is created from known pre- or post-mortem status PERSON: Chris Stoeckert, Jie Zheng MO_84 OrganismStatus - specimen with pre- or post-mortem status + specimen with pre- or post-mortem status @@ -65257,7 +65293,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + assay for transposase-accessible chromatin using sequencing Kasinathan et al., (February 2014). "High-resolution mapping of transcription factor binding sites on natitve chromatin." Nat Methods 11(2):203-9. doi: 10.1038/nmeth.2766. @@ -68028,8 +68064,7 @@ https://www.doi.org/ - - + @@ -68039,13 +68074,14 @@ https://www.doi.org/ - - H&E-stained fixed tissue slide specimen + + + H&E-stained fixed tissue slide specimen A fixed tissue slide specimen that is the output of H&E slide staining. - Chris Stoeckert, Ned Haubein - OBIB, OBI - H&E-stained fixed tissue slide specimen + Chris Stoeckert, Ned Haubein + OBIB, OBI + H&E-stained fixed tissue slide specimen @@ -68053,8 +68089,7 @@ https://www.doi.org/ - - + @@ -68064,14 +68099,14 @@ https://www.doi.org/ - - IHC-stained fixed tissue slide specimen + + + IHC-stained fixed tissue slide specimen A fixed tissue slide specimen that is the output of immunohistochemistry slide staining. - Chris Stoeckert, Ned Haubein - immunohistochemistry slide specimen - OBIB, OBI - IHC-stained fixed tissue slide specimen + Chris Stoeckert, Ned Haubein + OBIB, OBI + IHC-stained fixed tissue slide specimen @@ -68080,13 +68115,13 @@ https://www.doi.org/ - single cell specimen + single cell specimen A cell specimen that contains only one cell. Requested by Sirarat Sarntivijai (EBI). Details see tracker: https://sourceforge.net/p/obi/obi-terms/828/ PERSON: Jie Zheng, Alexander Diehl PERSON: Jie Zheng, Alexander Diehl - single cell specimen + single cell specimen @@ -73146,9 +73181,9 @@ https://www.doi.org/ + - @@ -73159,15 +73194,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -73188,9 +73218,9 @@ https://www.doi.org/ + - @@ -73201,15 +73231,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -73230,9 +73255,9 @@ https://www.doi.org/ + - @@ -73243,15 +73268,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -73272,9 +73292,9 @@ https://www.doi.org/ + - @@ -73285,15 +73305,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -73315,9 +73330,9 @@ https://www.doi.org/ + - @@ -73328,15 +73343,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -73358,9 +73368,9 @@ https://www.doi.org/ + - @@ -73371,15 +73381,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -73400,9 +73405,9 @@ https://www.doi.org/ + - @@ -73413,15 +73418,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -73442,9 +73442,9 @@ https://www.doi.org/ + - @@ -73455,15 +73455,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -73484,9 +73479,9 @@ https://www.doi.org/ + - @@ -73497,15 +73492,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -73526,9 +73516,9 @@ https://www.doi.org/ + - @@ -73539,15 +73529,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -73568,9 +73553,9 @@ https://www.doi.org/ + - @@ -73581,15 +73566,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -73610,9 +73590,9 @@ https://www.doi.org/ + - @@ -73633,15 +73613,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -73663,9 +73638,9 @@ https://www.doi.org/ + - @@ -73676,15 +73651,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -73705,9 +73675,9 @@ https://www.doi.org/ + - @@ -73728,15 +73698,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -73757,9 +73722,9 @@ https://www.doi.org/ + - @@ -73770,15 +73735,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -73799,9 +73759,9 @@ https://www.doi.org/ + - @@ -73812,15 +73772,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -73841,9 +73796,9 @@ https://www.doi.org/ + - @@ -73864,15 +73819,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -73893,9 +73843,9 @@ https://www.doi.org/ + - @@ -73906,15 +73856,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -73935,9 +73880,9 @@ https://www.doi.org/ + - @@ -73958,15 +73903,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -73987,9 +73927,9 @@ https://www.doi.org/ + - @@ -74000,15 +73940,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -74029,9 +73964,9 @@ https://www.doi.org/ + - @@ -74052,15 +73987,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -74081,9 +74011,9 @@ https://www.doi.org/ + - @@ -74104,15 +74034,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -74134,9 +74059,9 @@ https://www.doi.org/ + - @@ -74157,15 +74082,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -74186,9 +74106,9 @@ https://www.doi.org/ + - @@ -74209,15 +74129,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -74239,9 +74154,9 @@ https://www.doi.org/ + - @@ -74262,15 +74177,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -74291,9 +74201,9 @@ https://www.doi.org/ + - @@ -74314,15 +74224,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -74343,9 +74248,9 @@ https://www.doi.org/ + - @@ -74366,15 +74271,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -74396,9 +74296,9 @@ https://www.doi.org/ + - @@ -74419,15 +74319,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -74448,9 +74343,9 @@ https://www.doi.org/ + - @@ -74471,15 +74366,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -74500,9 +74390,9 @@ https://www.doi.org/ + - @@ -74523,15 +74413,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -74552,9 +74437,9 @@ https://www.doi.org/ + - @@ -74565,15 +74450,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -74594,9 +74474,9 @@ https://www.doi.org/ + - @@ -74617,15 +74497,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -74647,9 +74522,9 @@ https://www.doi.org/ + - @@ -74670,15 +74545,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -74699,9 +74569,9 @@ https://www.doi.org/ + - @@ -74722,15 +74592,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -74751,9 +74616,9 @@ https://www.doi.org/ + - @@ -74774,15 +74639,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -74803,9 +74663,9 @@ https://www.doi.org/ + - @@ -74826,15 +74686,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -74856,9 +74711,9 @@ https://www.doi.org/ + - @@ -74879,15 +74734,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -74909,9 +74759,9 @@ https://www.doi.org/ + - @@ -74932,15 +74782,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -74961,9 +74806,9 @@ https://www.doi.org/ + - @@ -74984,15 +74829,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -75014,9 +74854,9 @@ https://www.doi.org/ + - @@ -75037,15 +74877,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -75066,9 +74901,9 @@ https://www.doi.org/ + - @@ -75089,15 +74924,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -75118,9 +74948,9 @@ https://www.doi.org/ + - @@ -75141,15 +74971,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -75170,9 +74995,9 @@ https://www.doi.org/ + - @@ -75193,15 +75018,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -75222,9 +75042,9 @@ https://www.doi.org/ + - @@ -75245,15 +75065,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -75274,9 +75089,9 @@ https://www.doi.org/ + - @@ -75297,15 +75112,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -75326,9 +75136,9 @@ https://www.doi.org/ + - @@ -75349,15 +75159,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -75378,9 +75183,9 @@ https://www.doi.org/ + - @@ -75401,15 +75206,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -75430,9 +75230,9 @@ https://www.doi.org/ + - @@ -75453,15 +75253,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -75482,9 +75277,9 @@ https://www.doi.org/ + - @@ -75505,15 +75300,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -75534,9 +75324,9 @@ https://www.doi.org/ + - @@ -75557,15 +75347,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -75586,9 +75371,9 @@ https://www.doi.org/ + - @@ -75609,15 +75394,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -75638,9 +75418,9 @@ https://www.doi.org/ + - @@ -75661,15 +75441,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -75690,9 +75465,9 @@ https://www.doi.org/ + - @@ -75713,15 +75488,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -75742,9 +75512,9 @@ https://www.doi.org/ + - @@ -75765,15 +75535,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -75794,9 +75559,9 @@ https://www.doi.org/ + - @@ -75817,15 +75582,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -76195,7 +75955,6 @@ https://www.doi.org/ PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group - 2018-05-11T16:35:11Z polyA depleted RNA extract @@ -76664,10 +76423,15 @@ https://www.doi.org/ - - - - + + + + + + + + + swab specimen @@ -76732,37 +76496,29 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + areolar swab specimen @@ -76780,37 +76536,29 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + breast swab specimen @@ -76828,37 +76576,29 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + cheek swab specimen @@ -76876,37 +76616,29 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + nasopharyngeal swab specimen @@ -76924,37 +76656,29 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + oral swab specimen @@ -76972,37 +76696,29 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + oropharyngeal swab specimen @@ -77020,37 +76736,29 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + rectal swab specimen @@ -77068,37 +76776,29 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + tongue swab specimen @@ -77116,37 +76816,29 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + vagina swab specimen @@ -77164,37 +76856,29 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + fecal swab specimen @@ -77213,34 +76897,25 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -77515,7 +77190,7 @@ https://www.doi.org/ An extract of RNA which is produced through rRNA (ribosomal RNA) depletion (the removal of highly abundant rRNA species). Dan Berrios - https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4585-1 + https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4585-1 ribosomal RNA-depleted RNA extract @@ -78689,14 +78364,19 @@ https://www.doi.org/ + + + + + + + 1 + + + + + - - - - 1 - - - individual organism specimen A specimen composed of an individual organism to be studied in an investigation. @@ -80067,7 +79747,13 @@ https://www.doi.org/ - + + + + + + + arthropod meal of blood specimen A specimen used in a blood meal assay to determine what is the source of blood ingested by a mosquito. @@ -82063,7 +81749,6 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - @@ -82076,15 +81761,10 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - - - - - - - - - + + + + induced sputum specimen @@ -82670,11 +82350,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - platelet-poor plasma specimen + platelet-poor plasma specimen A blood plasma specimen that is the output of some platelet-poor plasma preparation and is the portion of plasma that contains fewer than 10,000 platelets per microliter. - PERSON: Matthew Diller - platelet-poor plasma specimen + PERSON: Matthew Diller + platelet-poor plasma specimen @@ -82725,38 +82405,28 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - - - - - - - - - + + + + - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + tracheal aspirate specimen @@ -82775,37 +82445,29 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + mid-turbinate nasal swab specimen @@ -82823,38 +82485,29 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + - + nasal aspirate specimen A specimen that is collected with a suctioning tube from the nasal cavity. @@ -82873,34 +82526,25 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -82922,37 +82566,29 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + upper respiratory specimen @@ -82970,7 +82606,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -82988,7 +82624,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + lower respiratory tract specimen A specimen that is derived from the lower respiratory tract. @@ -83005,37 +82641,29 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + anterior nasal swab specimen @@ -85083,7 +84711,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - @@ -85096,15 +84723,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - + + + + endotracheal tube specimen @@ -85123,7 +84745,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - @@ -85136,15 +84757,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - + + + + endotracheal aspirate specimen @@ -87298,11 +86914,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - @@ -87315,15 +86930,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - + + + + blood specimen in vacutainer @@ -87339,11 +86949,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - @@ -87356,15 +86965,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - + + + + blood specimen on filter paper @@ -91491,7 +91095,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + umbilical cord blood assay An assay that has an umbilical cord blood specimen as evaluant. @@ -92136,7 +91740,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + umbilical cord blood assay datum A data item that is the specified output of an umbilical cord blood assay. @@ -94999,9 +94603,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + - @@ -95012,19 +94616,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - + + + + - + placental blood specimen A specimen that is derived from placental blood. @@ -95669,11 +95268,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - @@ -95686,15 +95284,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - + + + + peripheral blood mononuclear cell specimen @@ -98036,7 +97629,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - @@ -98059,15 +97651,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - + + + + lymph specimen @@ -98086,7 +97673,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - @@ -98109,15 +97695,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - + + + + digestive tract specimen @@ -101456,6 +101037,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + serum anti-Epstein-Barr virus antibody level assay An antigen specific antibodies assay that is meant to detect antibodies that bind to Epstein-Barr virus (EBV) antigens in a serum sample. @@ -101510,6 +101092,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + serum anti-cytomegalovirus antibody level assay A CMV antibody assay that has serum as an input. @@ -101596,34 +101179,25 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -103097,24 +102671,29 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + + + + + + + + + + + - - - - - - - - - - albumin-free serum A blood serum specimen that contains no albumin. Sebastian Duesing https://github.com/obi-ontology/obi/issues/493 Philippe Rocca-Serra - albumin-free serum + albumin-free serum @@ -103543,7 +103122,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -103552,6 +103131,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + lavage fluid specimen The collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present. @@ -103569,34 +103149,25 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -103687,6 +103258,43 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + chromatin accessibility assay + + An assay that determines which regions of a DNA molecule are in the form of euchromatin and thus able to make direct physical contact with (i.e. are accessible to) other molecules such as RNA polymerase, transcription factors, etc. + Bjoern Peters + Michelle Giglio + Sebastian Duesing + Michelle Giglio + https://github.com/obi-ontology/obi/issues/1813 + Jennifer Jou + chromatin accessibility assay + + + + + + + + + m6A-MTase sequencing assay + https://pubmed.ncbi.nlm.nih.gov/32587015/ + + A DNA methylation profiling assay in which chromatin stencils are created by treating nuclei with m6A methyltransferase (MTase) and then sequenced using single-molecule circular consensus sequencing to identify regions of accessible DNA at nucleotide resolution. + Jennifer Jou + Sebastian Duesing + Fiber-seq + Jennifer Jou + https://github.com/obi-ontology/obi/issues/1813 + Jennifer Jou + m6A-MTase sequencing assay + + + + @@ -103777,18 +103385,8 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + - - - - - - - - - - - @@ -103805,17 +103403,17 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - blood plasma specimen - PMID: 18217225.Sex Transm Dis. 2008 Jan;35(1):55-60. Review.Human immunodeficiency virus viral load in blood plasma and semen: review and implications of empirical findings. + blood plasma specimen + PMID: 18217225.Sex Transm Dis. 2008 Jan;35(1):55-60. Review.Human immunodeficiency virus viral load in blood plasma and semen: review and implications of empirical findings. a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended. - 03/21/2010: BP, blood plasma is defined as the output of certain separation processes, so this is in the domain of OBI, not FMA. - PERSON: Maura Gasparetto - PERSON: Melanie Courtot + 03/21/2010: BP, blood plasma is defined as the output of certain separation processes, so this is in the domain of OBI, not FMA. + PERSON: Maura Gasparetto + PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra - plasma - WEB: http://en.wikipedia.org/wiki/Blood_plasma - blood plasma specimen + plasma + WEB: http://en.wikipedia.org/wiki/Blood_plasma + blood plasma specimen @@ -103823,7 +103421,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -103846,21 +103444,15 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - blood serum specimen - PMID: 18229666.Adv Med Sci. 2007;52 Suppl 1:204-6.Antioxidant activity of blood serum and saliva in patients with periodontal disease treated due to epilepsy. + blood serum specimen + PMID: 18229666.Adv Med Sci. 2007;52 Suppl 1:204-6.Antioxidant activity of blood serum and saliva in patients with periodontal disease treated due to epilepsy. A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors. - PERSON: Maura Gasparetto - PERSON: Melanie Courtot + PERSON: Maura Gasparetto + PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra - WEB: http://en.wikipedia.org/wiki/Blood_plasma - blood serum specimen + WEB: http://en.wikipedia.org/wiki/Blood_plasma + blood serum specimen @@ -104003,10 +103595,9 @@ This issue is outside the scope of OBI. specimen - Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. + Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen; collecting a stone from a site. - A material entity that has the specimen role. - Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. + A material entity that is collected for potential use as an input upon which measurements or observations are performed. PERSON: James Malone PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch @@ -104284,27 +103875,38 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ - - - - - - - - - - - - - - bronchial alveolar lavage - solution containing lung derived T cells, eosinophils, and TNFa. + + + + + + + + + + + + + + + + + + + + + + + + + bronchial alveolar lavage + solution containing lung derived T cells, eosinophils, and TNFa. Group of biomaterials present in the bronchial aveolar space of an organism which are collected through lavage including the reagents used to for the lavage process, organisms, cells, and cellular secretions present in the bronchial aveolar space. - PERSON: Bjoern Peters - BAL - GROUP: IEDB - bronchial alveolar lavage + PERSON: Bjoern Peters + BAL + GROUP: IEDB + bronchial alveolar lavage @@ -108401,13 +108003,13 @@ determinations of compounds. - pool of specimens + pool of specimens A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish. - check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish + check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish PERSON: Jennifer Fostel GROUP: CEBS - pool of specimens + pool of specimens @@ -115024,7 +114626,6 @@ Possible ecological risks of transgenic organism release when transgenes affect - @@ -115037,16 +114638,16 @@ Possible ecological risks of transgenic organism release when transgenes affect - whole mount tissue + whole mount tissue A whole organism preparation resulting from a histological preparation known as whole mount preparation where the whole specimen is mounted or spread on the microscope (glass) slide - PERSON: Helen Parkinson + PERSON: Helen Parkinson PERSON: Philippe Rocca-Serra - whole mount sample - GROUP: OBI - PRS:22-02-2008: indicates the need to create a protocol application and distinguish it from this entity - PRS:22-02-2008: is a material which has output_role during whole mount preparation protocol-application - whole mount tissue + whole mount sample + GROUP: OBI + PRS:22-02-2008: indicates the need to create a protocol application and distinguish it from this entity + PRS:22-02-2008: is a material which has output_role during whole mount preparation protocol-application + whole mount tissue @@ -115887,30 +115488,35 @@ Possible ecological risks of transgenic organism release when transgenes affect + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - lymph node cell specimen A cell specimen comprised of a mixed population of cells obtained by processing whole lymph node into individual cells, typically performed using a sieve. This population includes T cells, B cells, macrophages, and other cell types. - IEDB - IEDB - lymph node cell specimen + IEDB + IEDB + lymph node cell specimen @@ -116878,30 +116484,35 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - splenocyte specimen A cell specimen comprised of a mixed cell population obtained by processing whole spleen into individual cells, typically performed using a sieve or blender. This population includes T cells, B cells, macrophages, and other cell types. - IEDB - IEDB - splenocyte specimen + IEDB + IEDB + splenocyte specimen @@ -118957,15 +118568,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 FFPE specimen - Many of today’s researchers prefer to use Formalin-Fixed Paraffin-Embedded samples of tissues for their IHC, histological or in-situ genomic analyses. Professionally fixed and embedded FFPE samples and the biomolecules they contain are reasonably stable at ambient temperatures. - --based on https://lab-ally.com/histopathology-resources/ffpe-samples/ + Many of today’s researchers prefer to use Formalin-Fixed Paraffin-Embedded samples of tissues for their IHC, histological or in-situ genomic analyses. Professionally fixed and embedded FFPE samples and the biomolecules they contain are reasonably stable at ambient temperatures. -based on https://lab-ally.com/histopathology-resources/ffpe-samples/ A specimen that has been fixed in formalin and embedded in paraffin. MIABIS formalin-fixed paraffin-embeded specimen - - + https://www.biochain.com/general/what-is-ffpe-tissue/ + https://github.com/obi-ontology/obi/issues/1019 FFPE specimen @@ -118977,9 +118586,9 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - @@ -119000,15 +118609,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - + + + + @@ -119031,9 +118635,9 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - @@ -119054,15 +118658,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - + + + + @@ -119085,9 +118684,9 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - @@ -119098,15 +118697,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - + + + + @@ -119129,9 +118723,9 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - @@ -119152,15 +118746,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - + + + + @@ -119183,9 +118772,9 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - @@ -119206,15 +118795,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - + + + + @@ -119237,9 +118821,9 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - @@ -119260,15 +118844,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - + + + + @@ -119291,9 +118870,9 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - @@ -119314,15 +118893,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - + + + + @@ -119345,9 +118919,9 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - @@ -119368,15 +118942,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - + + + + @@ -119399,9 +118968,9 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - @@ -119412,15 +118981,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - + + + + @@ -119443,9 +119007,9 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - @@ -119456,15 +119020,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - + + + + @@ -119487,9 +119046,9 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - @@ -119510,15 +119069,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - + + + + @@ -119541,9 +119095,9 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - @@ -119554,15 +119108,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - + + + + @@ -119585,9 +119134,9 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - @@ -119598,15 +119147,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - + + + + @@ -119629,9 +119173,9 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - @@ -119642,19 +119186,14 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - + + + + - + arterial blood specimen A specimen that is derived from some arterial blood @@ -119673,9 +119212,9 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - @@ -119686,19 +119225,14 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - + + + + - + venous blood specimen A specimen that is derived from some venous blood @@ -119717,9 +119251,9 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - @@ -119730,19 +119264,14 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - + + + + - + capillary blood specimen A specimen that is derived from some capillary blood @@ -119758,38 +119287,29 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - - - - - - - - - + + + + - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + erythrocyte specimen @@ -119806,38 +119326,29 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - - - - - - - - - + + + + - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + reticulocyte specimen @@ -119854,38 +119365,29 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - - - - - - - - - + + + + - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + leukocyte specimen @@ -121842,6 +121344,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -121915,6 +121418,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -121988,6 +121492,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -122061,6 +121566,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -122135,6 +121641,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -122195,6 +121702,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -122255,6 +121763,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -122315,6 +121824,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -122375,6 +121885,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -122434,6 +121945,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -122508,6 +122020,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -122568,6 +122081,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -122628,6 +122142,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -122688,6 +122203,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -122747,6 +122263,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -122820,6 +122337,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -122893,6 +122411,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -122966,6 +122485,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -123039,6 +122559,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -123112,6 +122633,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -123185,6 +122707,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -123258,6 +122781,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -123332,6 +122856,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -123392,6 +122917,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -123452,6 +122978,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -123512,6 +123039,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -123571,6 +123099,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -123645,6 +123174,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -123704,6 +123234,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -123778,6 +123309,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -123850,6 +123382,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -123923,6 +123456,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -123996,6 +123530,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -124069,6 +123604,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -124142,6 +123678,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -124215,6 +123752,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -124288,6 +123826,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -124361,6 +123900,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -124434,6 +123974,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -124507,6 +124048,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -124580,6 +124122,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -124653,6 +124196,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -124726,6 +124270,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -124799,6 +124344,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -124873,6 +124419,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -124932,6 +124479,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -125006,6 +124554,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -125079,6 +124628,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -125139,6 +124689,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -125199,6 +124750,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -125259,6 +124811,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -125319,6 +124872,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -125379,6 +124933,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -125439,6 +124994,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -125499,6 +125055,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -125558,6 +125115,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -125631,6 +125189,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -125704,6 +125263,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -125777,6 +125337,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -125837,6 +125398,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -125910,6 +125472,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -125983,6 +125546,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -126056,6 +125620,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -126129,6 +125694,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -126202,7 +125768,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -126263,6 +125829,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -126335,6 +125902,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -126408,6 +125976,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -126481,6 +126050,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -126614,6 +126184,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -126687,6 +126258,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -126761,6 +126333,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -126820,6 +126393,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -126893,6 +126467,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -126966,6 +126541,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -127039,6 +126615,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -127112,6 +126689,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -127185,6 +126763,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -127258,6 +126837,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -127332,6 +126912,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -127391,6 +126972,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -127464,6 +127046,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -127538,6 +127121,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -127610,6 +127194,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -127966,6 +127551,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -128039,6 +127625,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -128112,6 +127699,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -128333,6 +127921,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -128394,6 +127983,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -128453,6 +128043,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -128526,6 +128117,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -128599,6 +128191,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -128672,6 +128265,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -128745,6 +128339,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -128818,6 +128413,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -128891,6 +128487,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -128964,6 +128561,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -129037,6 +128635,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -129110,6 +128709,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -129183,6 +128783,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -129256,6 +128857,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -129329,6 +128931,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -129402,6 +129005,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -129462,6 +129066,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -129522,6 +129127,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -129583,6 +129189,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -129642,6 +129249,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -129715,6 +129323,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -129788,6 +129397,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -129861,6 +129471,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -129934,6 +129545,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -130007,6 +129619,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -130081,6 +129694,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -130153,6 +129767,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -130227,6 +129842,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -130299,6 +129915,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -130372,6 +129989,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -130445,6 +130063,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -130518,7 +130137,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -130578,7 +130197,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -130638,7 +130257,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -130698,6 +130317,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -130771,6 +130391,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -130844,6 +130465,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -130917,6 +130539,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -130990,6 +130613,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -131063,6 +130687,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -131137,6 +130762,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -131196,6 +130822,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -131269,6 +130896,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -131343,6 +130971,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -131402,6 +131031,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -131475,6 +131105,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -131548,6 +131179,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -131621,6 +131253,7 @@ The content of that report on the IEDB website is here: 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http://iedb.org/refId/10 + @@ -132313,6 +131955,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -132386,6 +132029,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -132532,6 +132176,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -132605,6 +132250,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -132665,6 +132311,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -132738,6 +132385,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -132811,6 +132459,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -132884,6 +132533,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -132957,6 +132607,7 @@ The content of that report on the IEDB website is here: 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http://iedb.org/refId/10 + @@ -140593,6 +140339,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -140666,6 +140413,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -140739,6 +140487,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -140812,6 +140561,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -140885,6 +140635,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -140959,6 +140710,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -141018,6 +140770,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -141091,6 +140844,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -141164,6 +140918,7 @@ The content of that report on the IEDB website is here: 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http://iedb.org/refId/10 + @@ -142640,6 +142404,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -142713,6 +142478,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -142933,6 +142699,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -142992,6 +142759,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -143065,6 +142833,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -143138,7 +142907,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -143198,6 +142967,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -143271,6 +143041,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -143344,6 +143115,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -143405,6 +143177,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -143464,6 +143237,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -143538,6 +143312,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -143671,6 +143446,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -143745,6 +143521,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -143805,6 +143582,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -143865,6 +143643,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -143925,6 +143704,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -143985,6 +143765,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -144057,6 +143838,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -144130,6 +143912,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -144203,6 +143986,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -144263,6 +144047,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -144336,6 +144121,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -144409,6 +144195,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -144482,7 +144269,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -144542,6 +144329,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -144615,6 +144403,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -144689,6 +144478,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -144748,6 +144538,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -144821,6 +144612,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -144895,6 +144687,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -144954,6 +144747,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -145028,6 +144822,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -145087,6 +144882,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -145160,6 +144956,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -145233,6 +145030,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -145306,6 +145104,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -145379,6 +145178,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -145879,6 +145679,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -145952,6 +145753,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -146025,6 +145827,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -146098,6 +145901,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -146171,6 +145975,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -148193,6 +147998,18 @@ realizes some 'host of immune response role' + + + + + cloaca + Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures. + + cloaca + + + + diff --git a/views/NIAID-GSC-BRC.owl b/views/NIAID-GSC-BRC.owl index 1f196382..3ac385be 100644 --- a/views/NIAID-GSC-BRC.owl +++ b/views/NIAID-GSC-BRC.owl @@ -11,7 +11,7 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"> - + en Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester Alan Ruttenberg @@ -77,7 +77,7 @@ http://creativecommons.org/licenses/by/4.0/ Ontology for Biomedical Investigations Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2024-10-25 + 2024-12-05 @@ -2610,7 +2610,7 @@ Modification made by JZ. specimen role liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient. - a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation + A role borne by a material entity that is obtained during a specimen collection process and that can be realized by performing measurements or observations on the specimen. 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. blood taken from animal: animal continues in study, whereas blood has role specimen. @@ -3072,9 +3072,10 @@ that has_part some material entity is a material entity. If we add as equivalent specimen collection process - drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation + drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation, collecting a stone from a site - A planned process with the objective of collecting a specimen. + A planned process with the objective to obtain a material entity for potential use as an input upon which measurements or observations are performed. + Definition updated following discussion on 2024-10-07 OBI dev call. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. Philly2013: The specimen_role for the specimen is created during the specimen collection process. @@ -3095,10 +3096,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - - - - + @@ -3108,12 +3106,6 @@ http://sourceforge.net/p/obi/obi-terms/716/ - - - - - - sample from organism a material obtained from an organism in order to be a representative of the whole @@ -3180,7 +3172,8 @@ http://sourceforge.net/p/obi/obi-terms/716/ specimen collection objective The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. - A objective specification to obtain a material entity for potential use as an input during an investigation. + A objective specification that is fulfilled by obtaining a material entity for potential use as an input upon which measurements or observations are performed. + OBI recommends against subclassing this term in order to avoid further parallel hierarchies between this term and specimen collection process. Bjoern Peters Bjoern Peters specimen collection objective @@ -3237,7 +3230,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -3251,6 +3244,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ A material entity that has the material sample role OBI: workshop + sample sample population material sample @@ -3442,21 +3436,24 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + + + + + + processed specimen - A tissue sample that has been sliced and stained for a histology study. -A blood specimen that has been centrifuged to obtain the white blood cells. A specimen that has been intentionally physically modified. + A tissue sample that has been sliced and stained for a histology study. Bjoern Peters Bjoern Peters - A tissue sample that has been sliced and stained for a histology study. processed specimen @@ -3547,32 +3544,17 @@ In the examples above, a reagent is an operational component of a device, but th - - - - - - - - - - - - - - - - - + + nucleic acid extract An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. - PERSON: Jie Zheng + Person: Jie Zheng UPenn Group nucleic acid extract @@ -3711,32 +3693,63 @@ All subtype will be defined by textual definition now. + + + + + + + + + + + + + + + + cell specimen + + A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture. + Discussed on obi call Jan 23, 2017. To improve cell specimen that include single cell specimen. Details see tracker: https://sourceforge.net/p/obi/obi-terms/828 + PERSON: Chris Stoeckert, Jie Zheng, Alexander Diehl + MO_612 cell + cell specimen + + + + - - + + - - - - - - - + + + + + + + + + + + + - + - specimen with known storage state + specimen with known storage state A specimen for which it is known whether it has been subjected to storage of a specified type. PERSON: Chris Stoeckert, Jie Zheng MO_95 BiosourceType - specimen with known storage state + specimen with known storage state @@ -3747,18 +3760,26 @@ All subtype will be defined by textual definition now. + - - - - - + - - - - + + + + + + + + + + + + + + + @@ -3766,14 +3787,14 @@ All subtype will be defined by textual definition now. - specimen from organism + specimen from organism A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm). PERSON: Chris Stoeckert, Jie Zheng - tissue specimen + tissue specimen MO_954 organism_part CS16 - specimen from organism + specimen from organism @@ -5722,10 +5743,9 @@ This issue is outside the scope of OBI. specimen - Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. + Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen; collecting a stone from a site. - A material entity that has the specimen role. - Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. + A material entity that is collected for potential use as an input upon which measurements or observations are performed. PERSON: James Malone PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch @@ -5969,39 +5989,6 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from - - - - - - - - - - - - - - - - - - - - - - - collecting specimen from organism - taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient - - a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation - PERSON:Bjoern Peters - IEDB - collecting specimen from organism - - - - diff --git a/views/obi-base.owl b/views/obi-base.owl index b2770f24..28cc2006 100644 --- a/views/obi-base.owl +++ b/views/obi-base.owl @@ -13,7 +13,7 @@ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + en Ontology for Biomedical Investigations Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester @@ -80,7 +80,7 @@ http://creativecommons.org/licenses/by/4.0/ Ontology for Biomedical Investigations Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2024-10-03 + 2024-12-05 @@ -5725,7 +5725,7 @@ editor = PRS specimen role liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient. - a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation + A role borne by a material entity that is obtained during a specimen collection process and that can be realized by performing measurements or observations on the specimen. 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. blood taken from animal: animal continues in study, whereas blood has role specimen. @@ -13291,25 +13291,29 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + urine specimen a portion of urine collected from an organism @@ -13394,25 +13398,29 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + blood specimen blood drawn from a human for glucose assay @@ -13491,9 +13499,10 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation + drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation, collecting a stone from a site - A planned process with the objective of collecting a specimen. + A planned process with the objective to obtain a material entity for potential use as an input upon which measurements or observations are performed. + Definition updated following discussion on 2024-10-07 OBI dev call. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. Philly2013: The specimen_role for the specimen is created during the specimen collection process. @@ -13796,10 +13805,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - - - - + @@ -13807,13 +13813,6 @@ http://sourceforge.net/p/obi/obi-terms/716/ - - - - - - - sample from organism a material obtained from an organism in order to be a representative of the whole @@ -13939,24 +13938,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - - - - - - - - - - - - - - - - - - + @@ -14007,7 +13989,8 @@ http://sourceforge.net/p/obi/obi-terms/716/ The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. - A objective specification to obtain a material entity for potential use as an input during an investigation. + A objective specification that is fulfilled by obtaining a material entity for potential use as an input upon which measurements or observations are performed. + OBI recommends against subclassing this term in order to avoid further parallel hierarchies between this term and specimen collection process. Bjoern Peters Bjoern Peters specimen collection objective @@ -15941,7 +15924,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + @@ -15954,9 +15937,9 @@ the role 'adjuvant role' inheres in some 'material entity' a A material entity that has the material sample role OBI: workshop + sample sample population - - sample + https://github.com/obi-ontology/obi/issues/1013 material sample @@ -18177,39 +18160,42 @@ placeholder - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - pre-mortem specimen material obtained through a liver biopsy from a human patient a specimen that was taken from a live organism Bjoern Peters - MO_705 premortem + MO_705 premortem pre-mortem specimen @@ -18362,8 +18348,7 @@ placeholder Cytoplasmic RNA extraction from mammalian tissues to create cDNA library (Carninci P, Nakamura M, Sato K, Hayashizaki Y, Brownstein MJ. Cytoplasmic RNA extraction from fresh and frozen mammalian tissues. Biotechniques. 2002;33:306–309.) A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted. - PERSON: Chris Stoeckert - PERSON: Jie Zheng + PERSON:Chris Stoeckert UPenn Group cytoplasmic RNA extract @@ -18783,7 +18768,7 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. total RNA extract - Extraction of total RNA from cells with Qiagen mini RNeasy kit. + Extraction of total RNA from cells with Qiagen mini RNeasy kit A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen. PERSON: Chris Stoeckert @@ -18879,38 +18864,42 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - post mortem specimen the spleen taken from a dead mouse a specimen that was taken from a dead organism Bjoern Peters - MO_416 postmortem + MO_416 postmortem post mortem specimen @@ -19074,10 +19063,10 @@ Dev call Nov 22, 2010: To reflect this, the term's label has been updated t - - + + @@ -19093,23 +19082,16 @@ Dev call Nov 22, 2010: To reflect this, the term's label has been updated t - - + + - - - - - - - + labeled DNA extract a labeled specimen that is the output of a labeling process and has grain labeled DNA to be able to detect DNA in future experiments. - Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. -Added duirng Mar 1, 2010 dev call + Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call Group: OBI group Group: OBI group labeled DNA extract @@ -19120,19 +19102,33 @@ Added duirng Mar 1, 2010 dev call - - - - - - - - cloacal specimen + + + + + + + + + + + + + + + + + + + + + + + + cell specimen type of sample used in the PCIRN influenza network - A specimen obtained by inserting a swab deeply into the vent of the cloaca of -an organism and vigorously swabbing the wall. The swab should be deeply -stained with fecal material and is then placed in transport medium. + A specimen obtained by inserting a swab deeply into the vent of the cloaca of an organism and vigorously swabbing the wall. The swab should be deeply stained with fecal material and is then placed in transport medium. PERSON: Melanie Courtot WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf cloacal specimen @@ -19319,18 +19315,31 @@ stained with fecal material and is then placed in transport medium. - + + + + + + + + + + + + + + + - - + + nasopharyngeal aspirate specimen type of sample used in the PCIRN influenza network - A speciemn which derives from nasopharyngeal mucosa after -aspiration. + A specimen which derives from nasopharyngeal mucosa after aspiration. PERSON: Melanie Courtot WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf nasopharyngeal aspirate specimen @@ -19453,24 +19462,35 @@ Updated both textual and logical definition. Both input and output material of f - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + nasal swab specimen type of sample used in the PCIRN influenza network - A specimen obtained using a cotton swab on a stick, passed up the nostril to obtain a sample of -exudate and epithelial debris for microbiological or cellular examination. + A specimen obtained using a cotton swab on a stick, passed up the nostril to obtain a sample of exudate and epithelial debris for microbiological or cellular examination. PERSON: Melanie Courtot WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf nasal swab specimen @@ -19587,10 +19607,10 @@ exudate and epithelial debris for microbiological or cellular examination. - - + + @@ -19606,23 +19626,16 @@ exudate and epithelial debris for microbiological or cellular examination. - - + + - - - - - - - + labeled RNA extract a labeled specimen that is the output of a labeling process and has grain labeled RNA to be able to detect RNA in future experiments. - Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. -Added duirng Mar 1, 2010 dev call + Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call Group: OBI group Group: OBI group labeled RNA extract @@ -19636,6 +19649,7 @@ Added duirng Mar 1, 2010 dev call + @@ -19655,18 +19669,9 @@ Added duirng Mar 1, 2010 dev call - - - - - - - - - frozen specimen Frozen blood plasma @@ -20348,6 +20353,7 @@ Biochimie. 2010 Feb 18. + @@ -20367,17 +20373,9 @@ Biochimie. 2010 Feb 18. - - - - - - - - paraffin specimen liver tissue embedded in paraffin @@ -20466,19 +20464,22 @@ Biochimie. 2010 Feb 18. - + + + + + + processed specimen - A tissue sample that has been sliced and stained for a histology study. -A blood specimen that has been centrifuged to obtain the white blood cells. A specimen that has been intentionally physically modified. + A tissue sample that has been sliced and stained for a histology study. Bjoern Peters Bjoern Peters - A tissue sample that has been sliced and stained for a histology study. processed specimen @@ -20697,6 +20698,7 @@ A blood specimen that has been centrifuged to obtain the white blood cells. + @@ -20716,16 +20718,9 @@ A blood specimen that has been centrifuged to obtain the white blood cells. - - - - - - - lyophilized specimen freezing dried DNA @@ -20899,7 +20894,6 @@ In the examples above, a reagent is an operational component of a device, but th - fresh specimen a liver freshly removed from a rat @@ -21099,27 +21093,31 @@ In the examples above, a reagent is an operational component of a device, but th - - - - - - - - - + + + + + + + + + - - + + + + + + + - - - - - - + + + + + + - agar stab specimen a specimen that is output of a process that cell culture inoculated into agar for long term storage. @@ -21845,31 +21843,17 @@ JZ: based on textual definition of edited document, it can be defined as N&S - - - - - - - - - - - - - - - + - - + + nucleic acid extract An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. - PERSON: Jie Zheng + Person: Jie Zheng UPenn Group nucleic acid extract @@ -25339,10 +25323,10 @@ JZ: based on textual definition of edited document, it can be defined as N&S - - + + @@ -25358,25 +25342,18 @@ JZ: based on textual definition of edited document, it can be defined as N&S - - + + - - - - - - - + labeled nucleic acid extract a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments. Person: Jie Zheng labeled extract MO_221 labeledExtract - labeled extract labeled nucleic acid extract @@ -35275,26 +35252,24 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - - - - - - - - - - - - - cell specimen + + + + + + + + + + + + cell specimen A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture. - Discussed on obi call Jan 23, 2017. To improve cell specimen that include single cell specimen. Details see tracker: https://sourceforge.net/p/obi/obi-terms/828/ + Discussed on obi call Jan 23, 2017. To improve cell specimen that include single cell specimen. Details see tracker: https://sourceforge.net/p/obi/obi-terms/828 PERSON: Chris Stoeckert, Jie Zheng, Alexander Diehl MO_612 cell - cell specimen + cell specimen @@ -35370,27 +35345,31 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - + + - - - - - - - + + + + + + + + + + + + - + - - specimen with known storage state + specimen with known storage state A specimen for which it is known whether it has been subjected to storage of a specified type. PERSON: Chris Stoeckert, Jie Zheng MO_95 BiosourceType - specimen with known storage state + specimen with known storage state @@ -35633,31 +35612,38 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html + - - - - - + - - - - + + + + + + + + + + + + + + + - A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm). PERSON: Chris Stoeckert, Jie Zheng - tissue specimen + tissue specimen MO_954 organism_part - specimen from organism + specimen from organism @@ -36548,46 +36534,50 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - specimen with pre- or post-mortem status + specimen with pre- or post-mortem status A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism. organizational term, used in description of specimen that is created from known pre- or post-mortem status PERSON: Chris Stoeckert, Jie Zheng MO_84 OrganismStatus - specimen with pre- or post-mortem status + specimen with pre- or post-mortem status @@ -55098,14 +55088,20 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. + + + + + + Gravina, Michael T., Jenny H. Lin, and Stuart S. Levine. "Lane-by-lane sequencing using Illumina's Genome Analyzer II." BioTechniques 54.5 (2013): 265-269. PMID: 23662897 An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg + Genome Analyzer IIx Illumina GA IIx - Illumina Genome Analyzer IIx ENCODE group - Genome Analyzer IIx + Illumina Genome Analyzer IIx @@ -55113,7 +55109,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -55134,7 +55130,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -55166,9 +55162,9 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng - Illumina MiSeq + MiSeq http://res.illumina.com/documents/products/datasheets/datasheet_miseq.pdf - MiSeq + Illumina MiSeq @@ -56018,7 +56014,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -56027,9 +56023,9 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng - Illumina NextSeq 500 + NextSeq 500 http://systems.illumina.com/systems/nextseq-sequencer.html - NextSeq 500 + Illumina NextSeq 500 @@ -56037,7 +56033,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -56140,12 +56136,18 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. + + + + + + An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIe makes industry-leading next-generation sequencing technology accessible to more laboratories. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng + Genome Analyzer IIe Illumina GA IIe - Illumina Genome Analyzer IIe http://res.illumina.com/documents/products/datasheets/datasheet_genome_analyzer_iie.pdf - Genome Analyzer IIe + Illumina Genome Analyzer IIe @@ -56482,7 +56484,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + Kasinathan et al., (February 2014). "High-resolution mapping of transcription factor binding sites on natitve chromatin." Nat Methods 11(2):203-9. doi: 10.1038/nmeth.2766. An assay to capture the location of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution by Tn5 transposase insertion. Chris Stoeckert @@ -56685,7 +56687,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -56705,7 +56707,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -59063,7 +59065,7 @@ https://www.doi.org/ - + @@ -59073,13 +59075,13 @@ https://www.doi.org/ - - H&E-stained fixed tissue slide specimen + + H&E-stained fixed tissue slide specimen A fixed tissue slide specimen that is the output of H&E slide staining. - Chris Stoeckert, Ned Haubein - OBIB, OBI - H&E-stained fixed tissue slide specimen + Chris Stoeckert, Ned Haubein + OBIB, OBI + H&E-stained fixed tissue slide specimen @@ -59087,7 +59089,7 @@ https://www.doi.org/ - + @@ -59097,14 +59099,13 @@ https://www.doi.org/ - - IHC-stained fixed tissue slide specimen + + IHC-stained fixed tissue slide specimen A fixed tissue slide specimen that is the output of immunohistochemistry slide staining. - Chris Stoeckert, Ned Haubein - immunohistochemistry slide specimen - OBIB, OBI - IHC-stained fixed tissue slide specimen + Chris Stoeckert, Ned Haubein + OBIB, OBI + IHC-stained fixed tissue slide specimen @@ -59118,7 +59119,7 @@ https://www.doi.org/ Requested by Sirarat Sarntivijai (EBI). Details see tracker: https://sourceforge.net/p/obi/obi-terms/828/ PERSON: Jie Zheng, Alexander Diehl PERSON: Jie Zheng, Alexander Diehl - single cell specimen + single cell specimen @@ -59127,6 +59128,12 @@ https://www.doi.org/ + + + + + + Illumina Genome Analyzer A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. @@ -59141,7 +59148,13 @@ https://www.doi.org/ - + + + + + + + Illumina HiSeq X Ten A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. @@ -63767,9 +63780,9 @@ https://www.doi.org/ + - @@ -63780,15 +63793,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -63807,9 +63815,9 @@ https://www.doi.org/ + - @@ -63820,15 +63828,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -63847,9 +63850,9 @@ https://www.doi.org/ + - @@ -63860,15 +63863,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -63887,9 +63885,9 @@ https://www.doi.org/ + - @@ -63900,15 +63898,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -63928,9 +63921,9 @@ https://www.doi.org/ + - @@ -63941,15 +63934,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -63969,9 +63957,9 @@ https://www.doi.org/ + - @@ -63982,15 +63970,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -64009,9 +63992,9 @@ https://www.doi.org/ + - @@ -64022,15 +64005,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -64049,9 +64027,9 @@ https://www.doi.org/ + - @@ -64062,15 +64040,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -64089,9 +64062,9 @@ https://www.doi.org/ + - @@ -64102,15 +64075,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -64129,9 +64097,9 @@ https://www.doi.org/ + - @@ -64142,15 +64110,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -64169,9 +64132,9 @@ https://www.doi.org/ + - @@ -64182,15 +64145,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -64209,9 +64167,9 @@ https://www.doi.org/ + - @@ -64232,15 +64190,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -64260,9 +64213,9 @@ https://www.doi.org/ + - @@ -64273,15 +64226,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -64300,9 +64248,9 @@ https://www.doi.org/ + - @@ -64323,15 +64271,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -64350,9 +64293,9 @@ https://www.doi.org/ + - @@ -64363,15 +64306,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -64390,9 +64328,9 @@ https://www.doi.org/ + - @@ -64403,15 +64341,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -64430,9 +64363,9 @@ https://www.doi.org/ + - @@ -64453,15 +64386,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -64480,9 +64408,9 @@ https://www.doi.org/ + - @@ -64493,15 +64421,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -64520,9 +64443,9 @@ https://www.doi.org/ + - @@ -64543,15 +64466,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -64570,9 +64488,9 @@ https://www.doi.org/ + - @@ -64583,15 +64501,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -64610,9 +64523,9 @@ https://www.doi.org/ + - @@ -64633,15 +64546,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -64660,9 +64568,9 @@ https://www.doi.org/ + - @@ -64683,15 +64591,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -64711,9 +64614,9 @@ https://www.doi.org/ + - @@ -64734,15 +64637,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -64761,9 +64659,9 @@ https://www.doi.org/ + - @@ -64784,15 +64682,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -64812,9 +64705,9 @@ https://www.doi.org/ + - @@ -64835,15 +64728,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -64862,9 +64750,9 @@ https://www.doi.org/ + - @@ -64885,15 +64773,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -64912,9 +64795,9 @@ https://www.doi.org/ + - @@ -64935,15 +64818,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -64963,9 +64841,9 @@ https://www.doi.org/ + - @@ -64986,15 +64864,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -65013,9 +64886,9 @@ https://www.doi.org/ + - @@ -65036,15 +64909,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -65063,9 +64931,9 @@ https://www.doi.org/ + - @@ -65086,15 +64954,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -65113,9 +64976,9 @@ https://www.doi.org/ + - @@ -65126,15 +64989,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -65153,9 +65011,9 @@ https://www.doi.org/ + - @@ -65176,15 +65034,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -65204,9 +65057,9 @@ https://www.doi.org/ + - @@ -65227,15 +65080,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -65254,9 +65102,9 @@ https://www.doi.org/ + - @@ -65277,15 +65125,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -65304,9 +65147,9 @@ https://www.doi.org/ + - @@ -65327,15 +65170,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -65354,9 +65192,9 @@ https://www.doi.org/ + - @@ -65377,15 +65215,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -65405,9 +65238,9 @@ https://www.doi.org/ + - @@ -65428,15 +65261,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -65456,9 +65284,9 @@ https://www.doi.org/ + - @@ -65479,15 +65307,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -65506,9 +65329,9 @@ https://www.doi.org/ + - @@ -65529,15 +65352,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -65557,9 +65375,9 @@ https://www.doi.org/ + - @@ -65580,15 +65398,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -65607,9 +65420,9 @@ https://www.doi.org/ + - @@ -65630,15 +65443,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -65657,9 +65465,9 @@ https://www.doi.org/ + - @@ -65680,15 +65488,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -65707,9 +65510,9 @@ https://www.doi.org/ + - @@ -65730,15 +65533,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -65757,9 +65555,9 @@ https://www.doi.org/ + - @@ -65780,15 +65578,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -65807,9 +65600,9 @@ https://www.doi.org/ + - @@ -65830,15 +65623,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -65857,9 +65645,9 @@ https://www.doi.org/ + - @@ -65880,15 +65668,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -65907,9 +65690,9 @@ https://www.doi.org/ + - @@ -65930,15 +65713,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -65957,9 +65735,9 @@ https://www.doi.org/ + - @@ -65980,15 +65758,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -66007,9 +65780,9 @@ https://www.doi.org/ + - @@ -66030,15 +65803,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -66057,9 +65825,9 @@ https://www.doi.org/ + - @@ -66080,15 +65848,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -66107,9 +65870,9 @@ https://www.doi.org/ + - @@ -66130,15 +65893,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -66157,9 +65915,9 @@ https://www.doi.org/ + - @@ -66180,15 +65938,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -66207,9 +65960,9 @@ https://www.doi.org/ + - @@ -66230,15 +65983,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -66257,9 +66005,9 @@ https://www.doi.org/ + - @@ -66280,15 +66028,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -66307,9 +66050,9 @@ https://www.doi.org/ + - @@ -66330,15 +66073,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -66663,13 +66401,11 @@ https://www.doi.org/ - polyA depleted RNA extract A RNA extract that is the output of an extraction process in which RNA molecules lacking poly A tails at thier 3' ends are purified. Mark A. Miller, based on http://purl.obolibrary.org/obo/OBI_0000869 PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group - 2018-05-11T16:35:11Z polyA depleted RNA extract @@ -67096,12 +66832,16 @@ https://www.doi.org/ - - - - + + + + + + + + + - swab specimen A specimen that is stored on a swab as the output of a collecting specimen with swab process. @@ -67160,34 +66900,25 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -67206,34 +66937,25 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -67252,34 +66974,25 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -67298,34 +67011,25 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -67344,34 +67048,25 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -67390,34 +67085,25 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -67436,34 +67122,25 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -67482,34 +67159,25 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -67528,34 +67196,25 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -67574,34 +67233,25 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -67621,34 +67271,25 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -67901,7 +67542,7 @@ https://www.doi.org/ An extract of RNA which is produced through rRNA (ribosomal RNA) depletion (the removal of highly abundant rRNA species). Dan Berrios - https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4585-1 + https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4585-1 ribosomal RNA-depleted RNA extract @@ -67950,7 +67591,7 @@ https://www.doi.org/ - + @@ -69022,14 +68663,18 @@ https://www.doi.org/ - - - - - 1 - - - + + + + + + + 1 + + + + + A specimen composed of an individual organism to be studied in an investigation. Person: Jie Zheng EFO_0000542 individual @@ -70326,7 +69971,13 @@ https://www.doi.org/ - + + + + + + + A specimen used in a blood meal assay to determine what is the source of blood ingested by a mosquito. A specimen of the blood ingested by an arthropod. @@ -72249,10 +71900,10 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist + - @@ -72265,15 +71916,10 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - - - - - - - - - + + + + A sputum specimen that is collected from an organism following its inhalation of a nebulized salt solution. John Judkins @@ -72820,8 +72466,8 @@ b) that the amount of analyte/measurand detected is over some predetermined thre A blood plasma specimen that is the output of some platelet-poor plasma preparation and is the portion of plasma that contains fewer than 10,000 platelets per microliter. - PERSON: Matthew Diller - platelet-poor plasma specimen + PERSON: Matthew Diller + platelet-poor plasma specimen @@ -72866,37 +72512,28 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + - - - - - - - - - + + + + - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + A specimen that is collected with a suctioning tube from the trachea. Asiyah Yu Lin ORCID:0000-0003-2620-0345 @@ -72913,34 +72550,25 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -72958,34 +72586,25 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -73005,34 +72624,25 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -73051,34 +72661,25 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -73096,7 +72697,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -73128,34 +72729,25 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -75061,10 +74653,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + - @@ -75077,15 +74669,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - + + + + A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected upon removal of the tube from the trachea. John Judkins ORCID:0000-0001-6595-0902 @@ -75098,10 +74685,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + - @@ -75114,15 +74701,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - + + + + A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected by suction without removing the tube. John Judkins ORCID:0000-0001-6595-0902 @@ -77102,10 +76684,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + - @@ -77118,15 +76700,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - + + + + A blood specimen that is located in a vacutainer. John Judkins @@ -77140,10 +76717,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + - @@ -77156,15 +76733,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - + + + + A blood specimen that is located on a filter paper. Chris Stoeckert @@ -84103,9 +83675,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + - @@ -84116,15 +83688,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - + + + + @@ -84247,7 +83814,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -84271,7 +83838,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -84286,7 +83853,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre https://www.illumina.com/systems/sequencing-platforms/nextseq.html https://github.com/obi-ontology/obi/issues/1546 gEAR - NextSeq 550 + Illumina NextSeq 550 @@ -84737,10 +84304,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + - @@ -84753,15 +84320,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - + + + + A processed specimen that is extracted from whole blood using gradient centrifugation that separates the blood into a layer of peripheral blood mononuclear cells under the top layer of plasma. It contains lymphocytes, monocytes or macrophages that are critical components in the immune system. Chris Stoeckert @@ -86941,10 +86503,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + - @@ -86967,15 +86529,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - + + + + A specimen that is derived from a portion of lymph collected from an organism. John Judkins ORCID:0000-0001-6595-0902 @@ -86988,10 +86545,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + - @@ -87014,15 +86571,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - + + + + A specimen that is derived from part of a digestive tract. John Judkins ORCID:0000-0001-6595-0902 @@ -90269,34 +89821,25 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -90540,7 +90083,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -91626,23 +91169,27 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - + + + + + + + + + + + + + + + albumin-free serum A blood serum specimen that contains no albumin. Sebastian Duesing https://github.com/obi-ontology/obi/issues/493 Philippe Rocca-Serra - albumin-free serum + albumin-free serum @@ -92003,7 +91550,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -92026,7 +91573,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -92052,7 +91599,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -92076,34 +91623,25 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -92118,6 +91656,112 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + + + + + + + https://www.illumina.com/content/dam/illumina-support/documents//products/datasheets/datasheet_hiseq_systems.pdf + + A DNA Sequencer manufactured and/or marketed by Illumina and branded with the word HiSeq. + This class represents a series of instruments with various model names. There are several models in this series, including one that was simply called “HiSeq” as the model name. GENEPIO:0100110 ‘Illumina HiSeq’ may refer to a model, not the series. OBI may not have classes for all of the instruments in this series. + PERSON: Mark Andrew Miller + HiSeq series + PERSON: Mark Andrew Miller + https://github.com/obi-ontology/obi/issues/1825 + Alicia Clum + Illumina HiSeq Series Instrument + + + + + + + + + + + + + + + https://www.cd-genomics.com/blog/nextseq/ + + A DNA Sequencer manufactured and/or marketed by Illumina and branded with the word NextSeq. + This class represents a series of instruments with various model names. There are several models in this series. OBI may not have classes for all of the instruments in this series. It is unclear whether GENEPIO:0100126 ’Illumina NextSeq’ refers to the series or a model. + PERSON: Mark Andrew Miller + NextSeq series + PERSON: Mark Andrew Miller + https://github.com/obi-ontology/obi/issues/1825 + Alicia Clum + Illumina NextSeq Series Instrument + + + + + + + + + + + + + + + + A DNA Sequencer manufactured and/or marketed by Illumina and branded with the word NovaSeq. + This class represents a series of instruments with various model names. There are several models in this series. OBI may not have classes for all of the instruments in this series. It is unclear whether GENEPIO:0100122 ‘Illumina NovaSeq’ refers to the series or to a model. + PERSON: Mark Andrew Miller + NovaSeq series + PERSON: Mark Andrew Miller + https://github.com/obi-ontology/obi/issues/1825 + Alicia Clum + Illumina NovaSeq Series Instrument + + + + + + + + + chromatin accessibility assay + An assay that determines which regions of a DNA molecule are in the form of euchromatin and thus able to make direct physical contact with (i.e. are accessible to) other molecules such as RNA polymerase, transcription factors, etc. + Bjoern Peters + Michelle Giglio + Sebastian Duesing + Michelle Giglio + https://github.com/obi-ontology/obi/issues/1813 + Jennifer Jou + chromatin accessibility assay + + + + + + + + + m6A-MTase sequencing assay + https://pubmed.ncbi.nlm.nih.gov/32587015/ + A DNA methylation profiling assay in which chromatin stencils are created by treating nuclei with m6A methyltransferase (MTase) and then sequenced using single-molecule circular consensus sequencing to identify regions of accessible DNA at nucleotide resolution. + Jennifer Jou + Sebastian Duesing + Fiber-seq + Jennifer Jou + https://github.com/obi-ontology/obi/issues/1813 + Jennifer Jou + m6A-MTase sequencing assay + + + + @@ -92207,18 +91851,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - + @@ -92235,17 +91868,17 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - blood plasma specimen - PMID: 18217225.Sex Transm Dis. 2008 Jan;35(1):55-60. Review.Human immunodeficiency virus viral load in blood plasma and semen: review and implications of empirical findings. + blood plasma specimen + PMID: 18217225.Sex Transm Dis. 2008 Jan;35(1):55-60. Review.Human immunodeficiency virus viral load in blood plasma and semen: review and implications of empirical findings. a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended. - 03/21/2010: BP, blood plasma is defined as the output of certain separation processes, so this is in the domain of OBI, not FMA. - PERSON: Maura Gasparetto - PERSON: Melanie Courtot + 03/21/2010: BP, blood plasma is defined as the output of certain separation processes, so this is in the domain of OBI, not FMA. + PERSON: Maura Gasparetto + PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra - plasma - WEB: http://en.wikipedia.org/wiki/Blood_plasma - blood plasma specimen + plasma + WEB: http://en.wikipedia.org/wiki/Blood_plasma + blood plasma specimen @@ -92253,7 +91886,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -92276,21 +91909,15 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - blood serum specimen - PMID: 18229666.Adv Med Sci. 2007;52 Suppl 1:204-6.Antioxidant activity of blood serum and saliva in patients with periodontal disease treated due to epilepsy. + blood serum specimen + PMID: 18229666.Adv Med Sci. 2007;52 Suppl 1:204-6.Antioxidant activity of blood serum and saliva in patients with periodontal disease treated due to epilepsy. A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors. - PERSON: Maura Gasparetto - PERSON: Melanie Courtot + PERSON: Maura Gasparetto + PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra - WEB: http://en.wikipedia.org/wiki/Blood_plasma - blood serum specimen + WEB: http://en.wikipedia.org/wiki/Blood_plasma + blood serum specimen @@ -92430,10 +92057,9 @@ This issue is outside the scope of OBI. specimen - Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. + Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen; collecting a stone from a site. - A material entity that has the specimen role. - Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. + A material entity that is collected for potential use as an input upon which measurements or observations are performed. PERSON: James Malone PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch @@ -92706,27 +92332,37 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ - - - - - - - - - - - - - - bronchial alveolar lavage - solution containing lung derived T cells, eosinophils, and TNFa. + + + + + + + + + + + + + + + + + + + + + + + + bronchial alveolar lavage + solution containing lung derived T cells, eosinophils, and TNFa. Group of biomaterials present in the bronchial aveolar space of an organism which are collected through lavage including the reagents used to for the lavage process, organisms, cells, and cellular secretions present in the bronchial aveolar space. - PERSON: Bjoern Peters - BAL - GROUP: IEDB - bronchial alveolar lavage + PERSON: Bjoern Peters + BAL + GROUP: IEDB + bronchial alveolar lavage @@ -96797,14 +96433,13 @@ determinations of compounds. - - pool of specimens + pool of specimens A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish. - check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish + check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish PERSON: Jennifer Fostel GROUP: CEBS - pool of specimens + pool of specimens @@ -103395,16 +103030,16 @@ Possible ecological risks of transgenic organism release when transgenes affect - whole mount tissue + whole mount tissue A whole organism preparation resulting from a histological preparation known as whole mount preparation where the whole specimen is mounted or spread on the microscope (glass) slide - PERSON: Helen Parkinson + PERSON: Helen Parkinson PERSON: Philippe Rocca-Serra - whole mount sample - GROUP: OBI - PRS:22-02-2008: indicates the need to create a protocol application and distinguish it from this entity - PRS:22-02-2008: is a material which has output_role during whole mount preparation protocol-application - whole mount tissue + whole mount sample + GROUP: OBI + PRS:22-02-2008: indicates the need to create a protocol application and distinguish it from this entity + PRS:22-02-2008: is a material which has output_role during whole mount preparation protocol-application + whole mount tissue @@ -104234,29 +103869,33 @@ Possible ecological risks of transgenic organism release when transgenes affect - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + lymph node cell specimen A cell specimen comprised of a mixed population of cells obtained by processing whole lymph node into individual cells, typically performed using a sieve. This population includes T cells, B cells, macrophages, and other cell types. - IEDB - IEDB - lymph node cell specimen + IEDB + IEDB + lymph node cell specimen @@ -105205,29 +104844,33 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + splenocyte specimen A cell specimen comprised of a mixed cell population obtained by processing whole spleen into individual cells, typically performed using a sieve or blender. This population includes T cells, B cells, macrophages, and other cell types. - IEDB - IEDB - splenocyte specimen + IEDB + IEDB + splenocyte specimen @@ -107119,14 +106762,12 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 FFPE specimen - Many of today’s researchers prefer to use Formalin-Fixed Paraffin-Embedded samples of tissues for their IHC, histological or in-situ genomic analyses. Professionally fixed and embedded FFPE samples and the biomolecules they contain are reasonably stable at ambient temperatures. - --based on https://lab-ally.com/histopathology-resources/ffpe-samples/ + Many of today’s researchers prefer to use Formalin-Fixed Paraffin-Embedded samples of tissues for their IHC, histological or in-situ genomic analyses. Professionally fixed and embedded FFPE samples and the biomolecules they contain are reasonably stable at ambient temperatures. -based on https://lab-ally.com/histopathology-resources/ffpe-samples/ A specimen that has been fixed in formalin and embedded in paraffin. MIABIS formalin-fixed paraffin-embeded specimen - - + https://www.biochain.com/general/what-is-ffpe-tissue/ + https://github.com/obi-ontology/obi/issues/1019 FFPE specimen @@ -107138,9 +106779,9 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - @@ -107161,15 +106802,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - + + + + @@ -107189,9 +106825,9 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - @@ -107212,15 +106848,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - + + + + @@ -107240,9 +106871,9 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - @@ -107253,15 +106884,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - + + + + @@ -107281,9 +106907,9 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - @@ -107304,15 +106930,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - + + + + @@ -107332,9 +106953,9 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - @@ -107355,15 +106976,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - + + + + @@ -107383,9 +106999,9 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - @@ -107406,15 +107022,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - + + + + @@ -107434,9 +107045,9 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - @@ -107457,15 +107068,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - + + + + @@ -107485,9 +107091,9 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - @@ -107508,15 +107114,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - + + + + @@ -107536,9 +107137,9 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - @@ -107549,15 +107150,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - + + + + @@ -107577,9 +107173,9 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - @@ -107590,15 +107186,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - + + + + @@ -107618,9 +107209,9 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - @@ -107641,15 +107232,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - + + + + @@ -107669,9 +107255,9 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - @@ -107682,15 +107268,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - + + + + @@ -107710,9 +107291,9 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - @@ -107723,15 +107304,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - + + + + @@ -107751,9 +107327,9 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - @@ -107764,15 +107340,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - + + + + @@ -107792,9 +107363,9 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - @@ -107805,15 +107376,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - + + + + @@ -107833,9 +107399,9 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - @@ -107846,15 +107412,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - + + + + @@ -107871,37 +107432,28 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - - - - - - - - - + + + + - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + A specimen that is derived from some erythrocytes Christian Stoeckert ORCID:0000-0002-5714-991X @@ -107916,37 +107468,28 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - - - - - - - - - + + + + - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + A specimen that is derived from some reticulocytes Christian Stoeckert ORCID:0000-0002-5714-991X @@ -107961,37 +107504,28 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + - - - - - - - - - + + + + - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + A specimen that is derived from some leukocytes Christian Stoeckert ORCID:0000-0002-5714-991X @@ -134166,6 +133700,12 @@ realizes some 'host of immune response role' + + + + + + diff --git a/views/obi.obo b/views/obi.obo index 161f0f10..0b74ff38 100644 --- a/views/obi.obo +++ b/views/obi.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: 2024-10-25 -date: 25:10:2024 12:39 +data-version: 2024-12-05 +date: 05:12:2024 12:48 synonymtypedef: OMO:0003000 "abbreviation" synonymtypedef: OMO:0003001 "ambiguous synonym" synonymtypedef: OMO:0003002 "dubious synonym" @@ -80,7 +80,7 @@ property_value: http://purl.org/dc/elements/1.1/subject "An ontology for the ann property_value: http://purl.org/dc/terms/license "http://creativecommons.org/licenses/by/4.0/" xsd:string property_value: http://purl.org/dc/terms/title "Ontology for Biomedical Investigations" xsd:string property_value: IAO:0000589 "Ontology for Biomedical Investigations" xsd:string -property_value: owl:versionInfo "2024-10-25" xsd:string +property_value: owl:versionInfo "2024-12-05" xsd:string [Term] id: BFO:0000001 @@ -3854,7 +3854,7 @@ is_a: OBI:0000250 ! dye role [Term] id: OBI:0000112 name: specimen role -def: "a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation" [] +def: "A role borne by a material entity that is obtained during a specimen collection process and that can be realized by performing measurements or observations on the specimen." [] is_a: BFO:0000023 ! role [Term] @@ -4793,6 +4793,7 @@ is_a: BFO:0000023 ! role id: OBI:0000418 name: measuring glucose concentration in blood serum assay def: "An assay that determines the concentration of glucose molecules in a blood serum sample" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100020 ! glucose assay [Term] @@ -6170,7 +6171,7 @@ is_a: IAO:0000033 ! directive information entity [Term] id: OBI:0000659 name: specimen collection process -def: "A planned process with the objective of collecting a specimen." [] +def: "A planned process with the objective to obtain a material entity for potential use as an input upon which measurements or observations are performed." [] synonym: "specimen collection" EXACT [] is_a: OBI:0000011 ! planned process @@ -6314,7 +6315,7 @@ is_obsolete: true [Term] id: OBI:0000684 name: specimen collection objective -def: "A objective specification to obtain a material entity for potential use as an input during an investigation." [] +def: "A objective specification that is fulfilled by obtaining a material entity for potential use as an input upon which measurements or observations are performed." [] is_a: IAO:0000005 ! objective specification [Term] @@ -6554,7 +6555,7 @@ is_a: OBI:1110092 ! adjuvant role id: OBI:0000721 name: glucose tolerance test def: "An assay that measures glucose clearance from blood over time by repeated glucose measurement in blood serum or plasma after the administration of a glucose bolus in-vivo. This assay can be used to evaluate the severity of insulin resistance or the efficiency of glucose clearance." [] -is_a: OBI:0000070 ! assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:0000722 @@ -6964,7 +6965,7 @@ id: OBI:0000820 name: activated partial thromboplastin time assay def: "An assay that evaluates blood coagulation by measuring the time required for the appearance of fibrin strands following the mixing blood or plasma with phospholipid platelet substitute (e.g., crude cephalins, soybean phosphatides). It is a test of the intrinsic pathway (factors VIII, IX, XI, and XII) and the common pathway (fibrinogen, prothrombin, factors V and X) of blood coaguation . It is used as a screening test and to monitor heparin therapy." [] synonym: "aPTT assay" EXACT [] -is_a: OBI:0000070 ! assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:0000821 @@ -7244,13 +7245,13 @@ name: serum neutralization of viral infectivity assay def: "An analyte assay that measures virus-neutralizing abilities of different sera. Different dilutions of serum are mixed with virus and used to infect cells. At the lower dilutions, antibodies will block infection, but at higher dilutions, there will be too few antibodies to have an effect.The neutralization titer is expressed as the reciprocal of the highest dilution at which virus infection is blocked." [] synonym: "influenza neutralization assay" EXACT [] is_a: OBI:0000443 ! analyte assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:0000873 name: pre-mortem specimen def: "a specimen that was taken from a live organism" [] is_a: OBI:0001506 ! specimen with pre- or post-mortem status -disjoint_from: OBI:0000902 ! post mortem specimen [Term] id: OBI:0000874 @@ -7426,8 +7427,8 @@ is_a: OBI:0001143 ! labeled nucleic acid extract [Term] id: OBI:0000909 name: cloacal specimen -def: "A specimen obtained by inserting a swab deeply into the vent of the cloaca of\nan organism and vigorously swabbing the wall. The swab should be deeply\nstained with fecal material and is then placed in transport medium." [] -is_a: OBI:0100051 ! specimen +def: "A specimen obtained by inserting a swab deeply into the vent of the cloaca of an organism and vigorously swabbing the wall. The swab should be deeply stained with fecal material and is then placed in transport medium." [] +is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0000910 @@ -7459,8 +7460,8 @@ is_a: OBI:0000070 ! assay [Term] id: OBI:0000914 name: nasopharyngeal aspirate specimen -def: "A speciemn which derives from nasopharyngeal mucosa after\naspiration." [] -is_a: OBI:0100051 ! specimen +def: "A specimen which derives from nasopharyngeal mucosa after aspiration." [] +is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0000915 @@ -7478,7 +7479,8 @@ is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:0000917 name: nasal swab specimen -def: "A specimen obtained using a cotton swab on a stick, passed up the nostril to obtain a sample of\nexudate and epithelial debris for microbiological or cellular examination." [] +def: "A specimen obtained using a cotton swab on a stick, passed up the nostril to obtain a sample of exudate and epithelial debris for microbiological or cellular examination." [] +is_a: OBI:0001479 ! specimen from organism is_a: OBI:0002599 ! swab specimen [Term] @@ -7515,10 +7517,6 @@ id: OBI:0000922 name: frozen specimen def: "A specimen that has been frozen in order to store it." [] is_a: OBI:0001472 ! specimen with known storage state -disjoint_from: OBI:0000950 ! paraffin specimen -disjoint_from: OBI:0000965 ! lyophilized specimen -disjoint_from: OBI:0000971 ! fresh specimen -disjoint_from: OBI:0000981 ! agar stab specimen [Term] id: OBI:0000923 @@ -7697,9 +7695,6 @@ id: OBI:0000950 name: paraffin specimen def: "a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin" [] is_a: OBI:0001472 ! specimen with known storage state -disjoint_from: OBI:0000965 ! lyophilized specimen -disjoint_from: OBI:0000971 ! fresh specimen -disjoint_from: OBI:0000981 ! agar stab specimen [Term] id: OBI:0000951 @@ -7717,7 +7712,6 @@ is_a: OBI:0600007 ! administering substance in vivo id: OBI:0000953 name: processed specimen def: "A specimen that has been intentionally physically modified." [] -comment: A tissue sample that has been sliced and stained for a histology study. is_a: OBI:0000047 ! processed material is_a: OBI:0100051 ! specimen @@ -7788,8 +7782,6 @@ id: OBI:0000965 name: lyophilized specimen def: "a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage." [] is_a: OBI:0001472 ! specimen with known storage state -disjoint_from: OBI:0000971 ! fresh specimen -disjoint_from: OBI:0000981 ! agar stab specimen [Term] id: OBI:0000966 @@ -7829,7 +7821,6 @@ id: OBI:0000971 name: fresh specimen def: "a specimen that is output of a specimen creation process used for an investigation without storage." [] is_a: OBI:0001472 ! specimen with known storage state -disjoint_from: OBI:0000981 ! agar stab specimen [Term] id: OBI:0000972 @@ -8054,7 +8045,6 @@ is_obsolete: true id: OBI:0001010 name: nucleic acid extract def: "An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen." [] -is_a: OBI:0000423 ! extract is_a: OBI:0000953 ! processed specimen [Term] @@ -11014,7 +11004,7 @@ is_a: OBI:0001484 ! assay measuring T cell epitope specific in vivo activity id: OBI:0001468 name: cell specimen def: "A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture." [] -is_a: OBI:0100051 ! specimen +is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0001469 @@ -11266,7 +11256,7 @@ is_a: OBI:0600014 ! material component separation id: OBI:0001506 name: specimen with pre- or post-mortem status def: "A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism." [] -is_a: OBI:0100051 ! specimen +is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0001507 @@ -15089,7 +15079,7 @@ name: assay for transposase-accessible chromatin using sequencing def: "An assay to capture the location of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution by Tn5 transposase insertion." [] synonym: "ATAC-seq" EXACT [] synonym: "ATAC-seq assay" EXACT [] -is_a: OBI:0000070 ! assay +is_a: OBI:0003686 ! chromatin accessibility assay [Term] id: OBI:0002040 @@ -15727,7 +15717,6 @@ is_a: OMIABIS:0000052 ! fixed tissue slide specimen id: OBI:0002126 name: IHC-stained fixed tissue slide specimen def: "A fixed tissue slide specimen that is the output of immunohistochemistry slide staining." [] -synonym: "immunohistochemistry slide specimen" EXACT [] is_a: OMIABIS:0000052 ! fixed tissue slide specimen [Term] @@ -17810,54 +17799,63 @@ is_a: OBI:0000973 ! sequence data id: OBI:0002603 name: areolar swab specimen def: "A specimen that is collected with a swab from the surface of an areola of a breast." [] +is_a: OBI:0001479 ! specimen from organism is_a: OBI:0002599 ! swab specimen [Term] id: OBI:0002604 name: breast swab specimen def: "A specimen that is collected with a swab from the surface of a breast." [] +is_a: OBI:0001479 ! specimen from organism is_a: OBI:0002599 ! swab specimen [Term] id: OBI:0002605 name: cheek swab specimen def: "A specimen that is collected with a swab from the cheek portion of the inside surface of a mouth." [] +is_a: OBI:0001479 ! specimen from organism is_a: OBI:0002599 ! swab specimen [Term] id: OBI:0002606 name: nasopharyngeal swab specimen def: "A specimen that is collected with a swab from the surface of a nasopharynx." [] +is_a: OBI:0001479 ! specimen from organism is_a: OBI:0002599 ! swab specimen [Term] id: OBI:0002607 name: oral swab specimen def: "A specimen that is collected with a swab from the inside surface of a mouth." [] +is_a: OBI:0001479 ! specimen from organism is_a: OBI:0002599 ! swab specimen [Term] id: OBI:0002608 name: oropharyngeal swab specimen def: "A specimen that is collected with a swab from the surface of a oropharynx." [] +is_a: OBI:0001479 ! specimen from organism is_a: OBI:0002599 ! swab specimen [Term] id: OBI:0002609 name: rectal swab specimen def: "A specimen that is collected with a swab from the surface of a rectum." [] +is_a: OBI:0001479 ! specimen from organism is_a: OBI:0002599 ! swab specimen [Term] id: OBI:0002610 name: tongue swab specimen def: "A specimen that is collected with a swab from the surface of a tongue." [] +is_a: OBI:0001479 ! specimen from organism is_a: OBI:0002599 ! swab specimen [Term] id: OBI:0002611 name: vagina swab specimen def: "A specimen that is collected with a swab from the surface of a vagina." [] +is_a: OBI:0001479 ! specimen from organism is_a: OBI:0002599 ! swab specimen [Term] @@ -17865,6 +17863,7 @@ id: OBI:0002612 name: fecal swab specimen def: "A specimen that is collected with a swab from the surface of a feces." [] synonym: "stool swab specimen" EXACT [] +is_a: OBI:0001479 ! specimen from organism is_a: OBI:0002599 ! swab specimen [Term] @@ -18418,7 +18417,7 @@ id: OBI:0002691 name: arthropod meal of blood specimen def: "A specimen of the blood ingested by an arthropod." [] synonym: "blood meal" EXACT [] -is_a: OBI:0100051 ! specimen +is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002692 @@ -19007,12 +19006,13 @@ id: OBI:0002778 name: tracheal aspirate specimen def: "A specimen that is collected with a suctioning tube from the trachea." [] synonym: "tracheal wash specimen" EXACT [] -is_a: OBI:0100051 ! specimen +is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002779 name: mid-turbinate nasal swab specimen def: "A specimen that is collected with a mid-turbinate nasal swab from the turbinate area of the nasal cavity." [] +is_a: OBI:0001479 ! specimen from organism is_a: OBI:0002599 ! swab specimen [Term] @@ -19021,7 +19021,7 @@ name: nasal aspirate specimen def: "A specimen that is collected with a suctioning tube from the nasal cavity." [] synonym: "nasal wash specimen" EXACT [] synonym: "nasopharyngeal aspirate" EXACT [] -is_a: OBI:0100051 ! specimen +is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002781 @@ -19034,18 +19034,20 @@ is_a: OBI:0002783 ! lower respiratory tract specimen id: OBI:0002782 name: upper respiratory specimen def: "A specimen that is derived from the upper respiratory tract" [] +is_a: OBI:0001479 ! specimen from organism is_a: OBI:0002599 ! swab specimen [Term] id: OBI:0002783 name: lower respiratory tract specimen def: "A specimen that is derived from the lower respiratory tract." [] -is_a: OBI:0100051 ! specimen +is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002784 name: anterior nasal swab specimen def: "A specimen that is derived from the anterior nasal wall" [] +is_a: OBI:0001479 ! specimen from organism is_a: OBI:0002599 ! swab specimen [Term] @@ -20327,14 +20329,14 @@ id: OBI:0003054 name: blood specimen in vacutainer def: "A blood specimen that is located in a vacutainer." [] synonym: "Vacutainer sample" EXACT [] -is_a: OBI:2000009 ! bodily fluid specimen +is_a: OBI:0000655 ! blood specimen [Term] id: OBI:0003055 name: blood specimen on filter paper def: "A blood specimen that is located on a filter paper." [] synonym: "Filter paper sample" EXACT [] -is_a: OBI:2000009 ! bodily fluid specimen +is_a: OBI:0000655 ! blood specimen [Term] id: OBI:0003056 @@ -21391,7 +21393,7 @@ is_a: OBI:0000070 ! assay id: OBI:0003238 name: umbilical cord blood assay def: "An assay that has an umbilical cord blood specimen as evaluant." [] -is_a: OBI:0000070 ! assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:0003239 @@ -21527,7 +21529,7 @@ is_a: OBI:0003064 ! organism detection datum id: OBI:0003259 name: umbilical cord blood assay datum def: "A data item that is the specified output of an umbilical cord blood assay." [] -is_a: IAO:0000027 ! data item +is_a: OBI:0003243 ! blood assay datum [Term] id: OBI:0003260 @@ -22240,7 +22242,7 @@ is_a: OBI:0003366 ! organism diagnostic process id: OBI:0003380 name: placental blood specimen def: "A specimen that is derived from placental blood." [] -is_a: OBI:2000009 ! bodily fluid specimen +is_a: OBI:0000655 ! blood specimen [Term] id: OBI:0003381 @@ -22407,7 +22409,7 @@ id: OBI:0003415 name: peripheral blood mononuclear cell specimen def: "A processed specimen that is extracted from whole blood using gradient centrifugation that separates the blood into a layer of peripheral blood mononuclear cells under the top layer of plasma. It contains lymphocytes, monocytes or macrophages that are critical components in the immune system." [] synonym: "PBMC specimen" EXACT [] -is_a: OBI:0100051 ! specimen +is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0003416 @@ -23389,6 +23391,7 @@ name: serum anti-Epstein-Barr virus antibody level assay def: "An antigen specific antibodies assay that is meant to detect antibodies that bind to Epstein-Barr virus (EBV) antigens in a serum sample." [] synonym: "EBV" EXACT [] is_a: OBI:0002145 ! antigen specific antibodies assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:0003590 @@ -23396,6 +23399,7 @@ name: serum anti-cytomegalovirus antibody level assay def: "A CMV antibody assay that has serum as an input." [] synonym: "CMV" EXACT [] is_a: OBI:0002154 ! CMV antibody assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:0003591 @@ -23857,6 +23861,7 @@ id: OBI:0003666 name: lavage fluid specimen def: "A specimen obtained through a lavage process which includes fluid in addition to cells and/or cellular secretions." [] is_a: OBI:0000953 ! processed specimen +is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0003667 @@ -23886,6 +23891,19 @@ def: "A DNA Sequencer manufactured and/or marketed by Illumina and branded with synonym: "NovaSeq series" EXACT [] is_a: OBI:0400103 ! DNA sequencer +[Term] +id: OBI:0003686 +name: chromatin accessibility assay +def: "An assay that determines which regions of a DNA molecule are in the form of euchromatin and thus able to make direct physical contact with (i.e. are accessible to) other molecules such as RNA polymerase, transcription factors, etc." [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:0003687 +name: m6A-MTase sequencing assay +def: "A DNA methylation profiling assay in which chromatin stencils are created by treating nuclei with m6A methyltransferase (MTase) and then sequenced using single-molecule circular consensus sequencing to identify regions of accessible DNA at nucleotide resolution." [] +synonym: "Fiber-seq" EXACT [] +is_a: OBI:0003686 ! chromatin accessibility assay + [Term] id: OBI:0005246 name: injection function @@ -23916,13 +23934,14 @@ id: OBI:0100016 name: blood plasma specimen def: "a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended." [] synonym: "plasma" EXACT [] +is_a: OBI:0000655 ! blood specimen is_a: OBI:0000953 ! processed specimen [Term] id: OBI:0100017 name: blood serum specimen def: "A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors." [] -is_a: OBI:0000953 ! processed specimen +is_a: OBI:0100016 ! blood plasma specimen [Term] id: OBI:0100026 @@ -23954,7 +23973,7 @@ is_a: OBI:0302729 ! chemical solution [Term] id: OBI:0100051 name: specimen -def: "A material entity that has the specimen role." [] +def: "A material entity that is collected for potential use as an input upon which measurements or observations are performed." [] is_a: BFO:0000040 ! material entity [Term] @@ -24037,7 +24056,7 @@ id: OBI:0100067 name: bronchial alveolar lavage def: "Group of biomaterials present in the bronchial aveolar space of an organism which are collected through lavage including the reagents used to for the lavage process, organisms, cells, and cellular secretions present in the bronchial aveolar space." [] synonym: "BAL" EXACT [] -is_a: OBI:0100051 ! specimen +is_a: OBI:0003666 ! lavage fluid specimen [Term] id: OBI:0100069 @@ -26959,7 +26978,6 @@ def: "A whole organism preparation resulting from a histological preparation kno synonym: "whole mount sample" EXACT [] is_a: OBI:0000680 ! whole organism preparation is_a: OBI:0000953 ! processed specimen -is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:1000207 @@ -27927,36 +27945,39 @@ is_a: OBI:2000013 ! arterial blood specimen id: OBI:2000013 name: arterial blood specimen def: "A specimen that is derived from some arterial blood" [] -is_a: OBI:2000009 ! bodily fluid specimen +is_a: OBI:0000655 ! blood specimen [Term] id: OBI:2000014 name: venous blood specimen def: "A specimen that is derived from some venous blood" [] -is_a: OBI:2000009 ! bodily fluid specimen +is_a: OBI:0000655 ! blood specimen [Term] id: OBI:2000015 name: capillary blood specimen def: "A specimen that is derived from some capillary blood" [] -is_a: OBI:2000009 ! bodily fluid specimen +is_a: OBI:0000655 ! blood specimen [Term] id: OBI:2000016 name: erythrocyte specimen def: "A specimen that is derived from some erythrocytes" [] +is_a: OBI:0001479 ! specimen from organism is_a: OBI:0002599 ! swab specimen [Term] id: OBI:2000017 name: reticulocyte specimen def: "A specimen that is derived from some reticulocytes" [] +is_a: OBI:0001479 ! specimen from organism is_a: OBI:0002599 ! swab specimen [Term] id: OBI:2000018 name: leukocyte specimen def: "A specimen that is derived from some leukocytes" [] +is_a: OBI:0001479 ! specimen from organism is_a: OBI:0002599 ! swab specimen [Term] @@ -28269,24 +28290,28 @@ is_a: OBI:0000443 ! analyte assay id: OBI:2100052 name: panel5 venous blood carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a panel5 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100001 ! carbon dioxide assay [Term] id: OBI:2100053 name: panel5 venous blood sodium assay def: "An analyte assay that measures the abundance of sodium in venous blood as part of a panel5 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100002 ! sodium(1+) assay [Term] id: OBI:2100054 name: panel5 venous blood creatinine assay def: "An analyte assay that measures the abundance of creatinine in venous blood as part of a panel5 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100003 ! creatinine assay [Term] id: OBI:2100055 name: panel5 venous blood potassium assay def: "An analyte assay that measures the abundance of potassium in venous blood as part of a panel5 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100004 ! potassium(1+) assay [Term] @@ -28294,35 +28319,41 @@ id: OBI:2100056 name: automated differential venous blood basophil count assay def: "A cytometry assay that measures the count of basophils in venous blood as part of a automated differential order" [] is_a: OBI:0003021 ! basophil assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100057 name: automated differential venous blood neutrophil count assay def: "A cytometry assay that measures the count of neutrophils in venous blood as part of a automated differential order" [] is_a: OBI:0003022 ! neutrophil assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100058 name: automated differential venous blood eosinophil count assay def: "A cytometry assay that measures the count of eosinophils in venous blood as part of a automated differential order" [] is_a: OBI:0003023 ! eosinophil assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100059 name: automated differential venous blood lymphocyte count assay def: "A cytometry assay that measures the count of lymphocytes in venous blood as part of a automated differential order" [] is_a: OBI:0003024 ! lymphocyte assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100060 name: automated differential venous blood monocyte count assay def: "A cytometry assay that measures the count of monocytes in venous blood as part of a automated differential order" [] is_a: OBI:0003025 ! monocyte assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100061 name: venous blood chloride assay def: "An analyte assay that measures the abundance of chloride in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100010 ! chloride assay [Term] @@ -28330,71 +28361,83 @@ id: OBI:2100062 name: CBC with automated differential venous blood RBC count assay def: "A cytometry assay that measures the count of RBCs in venous blood as part of a CBC with automated differential order" [] is_a: OBI:0003018 ! hematocrit assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100063 name: CBC with automated differential venous blood platelet count assay def: "A cytometry assay that measures the count of platelets in venous blood as part of a CBC with automated differential order" [] is_a: OBI:0003028 ! platelet assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100064 name: CBC with automated differential venous blood WBC count assay def: "A cytometry assay that measures the count of WBCs in venous blood as part of a CBC with automated differential order" [] is_a: OBI:0001977 ! cytometry assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100065 name: CBC with automated differential venous blood hematocrit assay def: "A cytometry assay that measures the proportion of red blood cells in venous blood as part of a CBC with automated differential order" [] is_a: OBI:0003018 ! hematocrit assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100066 name: CBC with automated differential venous blood hemoglobin assay def: "An analyte assay that measures the abundance of hemoglobin in venous blood as part of a CBC with automated differential order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100014 ! hemoglobin assay [Term] id: OBI:2100067 name: venous blood phosphate assay def: "An analyte assay that measures the abundance of phosphate in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100015 ! phosphate ion assay [Term] id: OBI:2100068 name: liver injury venous blood alanine aminotransferase assay def: "An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a liver injury order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100016 ! alanine aminotransferase assay [Term] id: OBI:2100069 name: liver injury venous blood human alkaline phosphatase assay def: "An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a liver injury order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100017 ! alkaline phosphatase (human) assay [Term] id: OBI:2100070 name: liver injury venous blood bilirubin assay def: "An analyte assay that measures the abundance of bilirubin in venous blood as part of a liver injury order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100018 ! bilirubin IXalpha assay [Term] id: OBI:2100071 name: liver injury venous blood human aspartate aminotransferase assay def: "An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver injury order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100019 ! aspartate aminotransferase (human) assay [Term] id: OBI:2100072 name: venous blood glucose assay def: "An analyte assay that measures the abundance of glucose in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100020 ! glucose assay [Term] id: OBI:2100073 name: venous blood magnesium assay def: "An analyte assay that measures the abundance of magnesium in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100021 ! magnesium cation assay [Term] @@ -28402,29 +28445,34 @@ id: OBI:2100074 name: CBC venous blood RBC count assay def: "A cytometry assay that measures the count of RBCs in venous blood as part of a CBC order" [] is_a: OBI:0003018 ! hematocrit assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100075 name: CBC venous blood WBC count assay def: "A cytometry assay that measures the count of WBCs in venous blood as part of a CBC order" [] is_a: OBI:0001977 ! cytometry assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100076 name: CBC venous blood hematocrit assay def: "A cytometry assay that measures the proportion of red blood cells in venous blood as part of a CBC order" [] is_a: OBI:0003018 ! hematocrit assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100077 name: CBC venous blood platelet count assay def: "A cytometry assay that measures the count of platelets in venous blood as part of a CBC order" [] is_a: OBI:0003028 ! platelet assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100078 name: CBC venous blood hemoglobin assay def: "An analyte assay that measures the abundance of hemoglobin in venous blood as part of a CBC order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100014 ! hemoglobin assay [Term] @@ -28432,11 +28480,13 @@ id: OBI:2100079 name: corrected venous blood leukocyte count assay def: "A cytometry assay that measures the count of leukocytes in venous blood as part of a corrected order" [] is_a: OBI:0001977 ! cytometry assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100080 name: liver evaluation venous blood bilirubin assay def: "An analyte assay that measures the abundance of bilirubin in venous blood as part of a liver evaluation order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100018 ! bilirubin IXalpha assay [Term] @@ -28444,89 +28494,104 @@ id: OBI:2100081 name: liver evaluation venous blood globulin assay def: "An analyte assay that measures the abundance of globulin in venous blood as part of a liver evaluation order" [] is_a: OBI:0003015 ! globulin assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100082 name: liver evaluation venous blood albumin assay def: "An analyte assay that measures the abundance of albumin in venous blood as part of a liver evaluation order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100022 ! albumin assay [Term] id: OBI:2100083 name: liver evaluation venous blood human aspartate aminotransferase assay def: "An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver evaluation order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100019 ! aspartate aminotransferase (human) assay [Term] id: OBI:2100084 name: liver evaluation venous blood alanine aminotransferase assay def: "An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a liver evaluation order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100016 ! alanine aminotransferase assay [Term] id: OBI:2100085 name: liver evaluation venous blood human alkaline phosphatase assay def: "An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a liver evaluation order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100017 ! alkaline phosphatase (human) assay [Term] id: OBI:2100086 name: liver evaluation venous blood protein assay def: "An analyte assay that measures the abundance of protein in venous blood as part of a liver evaluation order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100087 name: basic metabolic panel venous blood chloride assay def: "An analyte assay that measures the abundance of chloride in venous blood as part of a basic metabolic panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100010 ! chloride assay [Term] id: OBI:2100088 name: basic metabolic panel venous blood potassium assay def: "An analyte assay that measures the abundance of potassium in venous blood as part of a basic metabolic panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100004 ! potassium(1+) assay [Term] id: OBI:2100089 name: basic metabolic panel venous blood sodium assay def: "An analyte assay that measures the abundance of sodium in venous blood as part of a basic metabolic panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100002 ! sodium(1+) assay [Term] id: OBI:2100090 name: basic metabolic panel venous blood creatinine assay def: "An analyte assay that measures the abundance of creatinine in venous blood as part of a basic metabolic panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100003 ! creatinine assay [Term] id: OBI:2100091 name: basic metabolic panel venous blood glucose assay def: "An analyte assay that measures the abundance of glucose in venous blood as part of a basic metabolic panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100020 ! glucose assay [Term] id: OBI:2100092 name: basic metabolic panel venous blood calcium assay def: "An analyte assay that measures the abundance of calcium in venous blood as part of a basic metabolic panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100024 ! calcium cation assay [Term] id: OBI:2100093 name: basic metabolic panel venous blood carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a basic metabolic panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100001 ! carbon dioxide assay [Term] id: OBI:2100094 name: venous blood creatine kinase assay def: "An analyte assay that measures the abundance of creatine kinase in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100025 ! creatine kinase assay [Term] id: OBI:2100095 name: venous blood calcium assay def: "An analyte assay that measures the abundance of calcium in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100024 ! calcium cation assay [Term] @@ -28534,11 +28599,13 @@ id: OBI:2100096 name: venous blood ferritin assay def: "An assay that measures ferritin in venous blood" [] is_a: OBI:0003009 ! ferritin assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100097 name: total venous blood calcium assay def: "An analyte assay that measures the abundance of calcium in venous blood as part of a total order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100024 ! calcium cation assay [Term] @@ -28546,137 +28613,159 @@ id: OBI:2100098 name: venous blood iron assay def: "An analyte assay that measures the abundance of iron in venous blood" [] is_a: OBI:0003011 ! iron assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100099 name: CBC with manual differential venous blood band neutrophil count assay def: "A cytometry assay that measures the count of band neutrophils in venous blood as part of a CBC with manual differential order" [] is_a: OBI:0003022 ! neutrophil assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100100 name: CBC with manual differential venous blood WBC count assay def: "A cytometry assay that measures the count of WBCs in venous blood as part of a CBC with manual differential order" [] is_a: OBI:0001977 ! cytometry assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100101 name: CBC with manual differential venous blood eosinophil count assay def: "A cytometry assay that measures the count of eosinophils in venous blood as part of a CBC with manual differential order" [] is_a: OBI:0003023 ! eosinophil assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100102 name: CBC with manual differential venous blood lymphocyte count assay def: "A cytometry assay that measures the count of lymphocytes in venous blood as part of a CBC with manual differential order" [] is_a: OBI:0003024 ! lymphocyte assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100103 name: CBC with manual differential venous blood nucleated RBC count assay def: "A cytometry assay that measures the count of nucleated RBCs in venous blood as part of a CBC with manual differential order" [] is_a: OBI:0003018 ! hematocrit assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100104 name: CBC with manual differential venous blood monocyte count assay def: "A cytometry assay that measures the count of monocytes in venous blood as part of a CBC with manual differential order" [] is_a: OBI:0003025 ! monocyte assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100105 name: CBC with manual differential venous blood segmented neutrophil count assay def: "A cytometry assay that measures the count of segmented neutrophils in venous blood as part of a CBC with manual differential order" [] is_a: OBI:0003022 ! neutrophil assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100106 name: CBC with manual differential venous blood basophil count assay def: "A cytometry assay that measures the count of basophils in venous blood as part of a CBC with manual differential order" [] is_a: OBI:0003021 ! basophil assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100107 name: venous blood albumin assay def: "An analyte assay that measures the abundance of albumin in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100022 ! albumin assay [Term] id: OBI:2100108 name: cardiac enzymes venous blood creatine kinase assay def: "An analyte assay that measures the abundance of creatine kinase in venous blood as part of a cardiac enzymes order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100025 ! creatine kinase assay [Term] id: OBI:2100109 name: venous blood haptoglobin assay def: "An analyte assay that measures the abundance of haptoglobin in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100110 name: venous blood lactate dehydrogenase assay def: "An assay that measures lactate dehydrogenase in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100028 ! lactate dehydrogenase complex assay [Term] id: OBI:2100111 name: venous blood prealbunin assay def: "An analyte assay that measures the abundance of prealbunin in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100112 name: lipid panel venous blood triglyceride assay def: "An analyte assay that measures the abundance of triglyceride in venous blood as part of a lipid panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100029 ! triglyceride assay [Term] id: OBI:2100113 name: lipid panel venous blood high density lipoprotein assay def: "An analyte assay that measures the abundance of high density lipoprotein in venous blood as part of a lipid panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100030 ! high-density lipoprotein cholesterol assay [Term] id: OBI:2100114 name: lipid panel venous blood cholesterol assay def: "An analyte assay that measures the abundance of cholesterol in venous blood as part of a lipid panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100031 ! cholesterol assay [Term] id: OBI:2100115 name: lipid panel venous blood low density lipoprotein assay def: "An analyte assay that measures the abundance of low density lipoprotein in venous blood as part of a lipid panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100032 ! low-density lipoprotein cholesterol assay [Term] id: OBI:2100116 name: venous blood hemoglobin A1c assay def: "An assay that measures hemoglobin A1c in venous blood" [] -is_a: OBI:0000070 ! assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100117 name: venous blood uric acid assay def: "An analyte assay that measures the abundance of uric acid in venous blood" [] is_a: OBI:0003014 ! uric acid assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100118 name: total venous blood protein assay def: "An analyte assay that measures the abundance of protein in venous blood as part of a total order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100119 name: venous blood thyroid stimulating hormone assay def: "An analyte assay that measures the abundance of thyroid stimulating hormone in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100033 ! thyroid stimulating hormone assay [Term] id: OBI:2100120 name: venous blood prostate specific antigen assay def: "An analyte assay that measures the abundance of prostate specific antigen in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100034 ! prostate-specific antigen assay [Term] @@ -28689,12 +28778,14 @@ is_a: OBI:0003043 ! urine assay id: OBI:2100122 name: T4 uptake venous blood T4 assay def: "An analyte assay that measures the abundance of T4 in venous blood as part of a T4 uptake order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100035 ! thyroxine assay [Term] id: OBI:2100123 name: arterial blood glucose assay def: "An analyte assay that measures the abundance of glucose in arterial blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100020 ! glucose assay [Term] @@ -28702,47 +28793,55 @@ id: OBI:2100124 name: CBC with manual differential venous blood cell count assay def: "A cytometry assay that measures the count of cells in venous blood as part of a CBC with manual differential order" [] is_a: OBI:0001977 ! cytometry assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100125 name: hemoglobin oxygen saturation arterial blood oxygen assay def: "An analyte assay that measures the abundance of oxygen in arterial blood as part of a hemoglobin oxygen saturation order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100036 ! elemental oxygen assay [Term] id: OBI:2100126 name: hemoglobin oxygen saturation arterial blood hemoglobin assay def: "An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a hemoglobin oxygen saturation order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100014 ! hemoglobin assay [Term] id: OBI:2100127 name: inpatient profile venous blood sodium assay def: "An analyte assay that measures the abundance of sodium in venous blood as part of a inpatient profile order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100002 ! sodium(1+) assay [Term] id: OBI:2100128 name: inpatient profile venous blood creatinine assay def: "An analyte assay that measures the abundance of creatinine in venous blood as part of a inpatient profile order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100003 ! creatinine assay [Term] id: OBI:2100129 name: inpatient profile venous blood potassium assay def: "An analyte assay that measures the abundance of potassium in venous blood as part of a inpatient profile order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100004 ! potassium(1+) assay [Term] id: OBI:2100130 name: inpatient profile venous blood carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a inpatient profile order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100001 ! carbon dioxide assay [Term] id: OBI:2100131 name: venous blood folic acid assay def: "An analyte assay that measures the abundance of folic acid in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100037 ! folic acids assay [Term] @@ -28750,17 +28849,20 @@ id: OBI:2100132 name: count venous blood reticulocyte count assay def: "A cytometry assay that measures the count of reticulocytes in venous blood as part of a count order" [] is_a: OBI:0003026 ! reticulocyte assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100133 name: venous blood potassium assay def: "An analyte assay that measures the abundance of potassium in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100004 ! potassium(1+) assay [Term] id: OBI:2100134 name: venous blood carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100001 ! carbon dioxide assay [Term] @@ -28768,11 +28870,13 @@ id: OBI:2100135 name: venous blood transferrin assay def: "An analyte assay that measures the abundance of transferrin in venous blood" [] is_a: OBI:0003013 ! transferrin assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100136 name: venous blood sodium assay def: "An analyte assay that measures the abundance of sodium in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100002 ! sodium(1+) assay [Term] @@ -28807,18 +28911,21 @@ is_a: OBI:2100039 ! osmolality assay id: OBI:2100141 name: cooximitery arterial blood oxygen assay def: "An analyte assay that measures the abundance of oxygen in arterial blood as part of a cooximitery order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100036 ! elemental oxygen assay [Term] id: OBI:2100142 name: cooximitery arterial blood hemoglobin assay def: "An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a cooximitery order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100014 ! hemoglobin assay [Term] id: OBI:2100143 name: cooximitery arterial blood methemoglobin assay def: "An analyte assay that measures the abundance of methemoglobin in arterial blood as part of a cooximitery order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100040 ! methemoglobin assay [Term] @@ -28839,6 +28946,7 @@ is_a: OBI:2100004 ! potassium(1+) assay id: OBI:2100146 name: Biosite cardiac panel arterial blood creatine kinase MB assay def: "An assay that measures creatine kinase MB in arterial blood as part of a Biosite cardiac panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100041 ! cytosolic creatine kinase complex, MB-type assay [Term] @@ -28846,101 +28954,118 @@ id: OBI:2100147 name: venous blood fibrinogen assay def: "An assay that measures fibrinogen in venous blood" [] is_a: OBI:0003010 ! fibrinogen assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100148 name: comprehensive metabolic panel venous blood carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a comprehensive metabolic panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100001 ! carbon dioxide assay [Term] id: OBI:2100149 name: comprehensive metabolic panel venous blood calcium assay def: "An analyte assay that measures the abundance of calcium in venous blood as part of a comprehensive metabolic panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100024 ! calcium cation assay [Term] id: OBI:2100150 name: comprehensive metabolic panel venous blood potassium assay def: "An analyte assay that measures the abundance of potassium in venous blood as part of a comprehensive metabolic panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100004 ! potassium(1+) assay [Term] id: OBI:2100151 name: comprehensive metabolic panel venous blood sodium assay def: "An analyte assay that measures the abundance of sodium in venous blood as part of a comprehensive metabolic panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100002 ! sodium(1+) assay [Term] id: OBI:2100152 name: comprehensive metabolic panel venous blood glucose assay def: "An analyte assay that measures the abundance of glucose in venous blood as part of a comprehensive metabolic panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100020 ! glucose assay [Term] id: OBI:2100153 name: comprehensive metabolic panel venous blood albumin assay def: "An analyte assay that measures the abundance of albumin in venous blood as part of a comprehensive metabolic panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100022 ! albumin assay [Term] id: OBI:2100154 name: comprehensive metabolic panel venous blood human alkaline phosphatase assay def: "An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a comprehensive metabolic panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100017 ! alkaline phosphatase (human) assay [Term] id: OBI:2100155 name: comprehensive metabolic panel venous blood bilirubin assay def: "An analyte assay that measures the abundance of bilirubin in venous blood as part of a comprehensive metabolic panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100018 ! bilirubin IXalpha assay [Term] id: OBI:2100156 name: comprehensive metabolic panel venous blood chloride assay def: "An analyte assay that measures the abundance of chloride in venous blood as part of a comprehensive metabolic panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100010 ! chloride assay [Term] id: OBI:2100157 name: comprehensive metabolic panel venous blood human aspartate aminotransferase assay def: "An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a comprehensive metabolic panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100019 ! aspartate aminotransferase (human) assay [Term] id: OBI:2100158 name: comprehensive metabolic panel venous blood protein assay def: "An analyte assay that measures the abundance of protein in venous blood as part of a comprehensive metabolic panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100159 name: comprehensive metabolic panel venous blood creatinine assay def: "An analyte assay that measures the abundance of creatinine in venous blood as part of a comprehensive metabolic panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100003 ! creatinine assay [Term] id: OBI:2100160 name: comprehensive metabolic panel venous blood alanine aminotransferase assay def: "An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a comprehensive metabolic panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100016 ! alanine aminotransferase assay [Term] id: OBI:2100161 name: venous blood LDH assay def: "An assay that measures LDH in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100028 ! lactate dehydrogenase complex assay [Term] id: OBI:2100162 name: venous blood creatine kinase MB assay def: "An assay that measures creatine kinase MB in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100041 ! cytosolic creatine kinase complex, MB-type assay [Term] id: OBI:2100163 name: venous blood lactic acid assay def: "An assay that measures lactic acid in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100042 ! rac-lactic acid assay [Term] @@ -28948,41 +29073,48 @@ id: OBI:2100164 name: venous blood hematocrit assay def: "A cytometry assay that measures the proportion of red blood cells in venous blood" [] is_a: OBI:0003018 ! hematocrit assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100165 name: venous blood creatinine assay def: "An analyte assay that measures the abundance of creatinine in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100003 ! creatinine assay [Term] id: OBI:2100166 name: blood gas venous blood oxygen assay def: "An analyte assay that measures the abundance of oxygen in venous blood as part of a blood gas order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100036 ! elemental oxygen assay [Term] id: OBI:2100167 name: ionized venous blood ionized calcium assay def: "An analyte assay that measures the abundance of ionized calcium in venous blood as part of a ionized order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100024 ! calcium cation assay [Term] id: OBI:2100168 name: blood gas venous blood carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a blood gas order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100001 ! carbon dioxide assay [Term] id: OBI:2100169 name: blood gas venous blood bicarbonate assay def: "An analyte assay that measures the abundance of bicarbonate in venous blood as part of a blood gas order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100043 ! hydrogencarbonate assay [Term] id: OBI:2100170 name: arterial blood creatinine assay def: "An analyte assay that measures the abundance of creatinine in arterial blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100003 ! creatinine assay [Term] @@ -28990,11 +29122,13 @@ id: OBI:2100171 name: venous blood tacrolimus assay def: "An analyte assay that measures the abundance of tacrolimus in venous blood" [] is_a: OBI:0000443 ! analyte assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100172 name: random venous blood vancomycin assay def: "An analyte assay that measures the abundance of vancomycin in venous blood as part of a random order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100044 ! vancomycin assay [Term] @@ -29002,77 +29136,87 @@ id: OBI:2100173 name: venous blood mycophenolic acid assay def: "An analyte assay that measures the abundance of mycophenolic acid in venous blood" [] is_a: OBI:0000443 ! analyte assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100174 name: non-vented blood gas arterial blood carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a non-vented blood gas order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100001 ! carbon dioxide assay [Term] id: OBI:2100175 name: non-vented blood gas arterial blood oxygen assay def: "An analyte assay that measures the abundance of oxygen in arterial blood as part of a non-vented blood gas order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100036 ! elemental oxygen assay [Term] id: OBI:2100176 name: non-vented blood gas arterial blood bicarbonate assay def: "An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a non-vented blood gas order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100043 ! hydrogencarbonate assay [Term] id: OBI:2100177 name: quantitative venous blood IgG assay def: "An assay that measures IgG in venous blood as part of a quantitative order" [] -is_a: OBI:0000070 ! assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100178 name: quantitative venous blood IgM assay def: "An assay that measures IgM in venous blood as part of a quantitative order" [] -is_a: OBI:0000070 ! assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100179 name: quantitative venous blood IgA assay def: "An assay that measures IgA in venous blood as part of a quantitative order" [] -is_a: OBI:0000070 ! assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100180 name: arterial blood sodium assay def: "An analyte assay that measures the abundance of sodium in arterial blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100002 ! sodium(1+) assay [Term] id: OBI:2100181 name: arterial blood potassium assay def: "An analyte assay that measures the abundance of potassium in arterial blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100004 ! potassium(1+) assay [Term] id: OBI:2100182 name: ionized arterial blood calcium assay def: "An analyte assay that measures the abundance of calcium in arterial blood as part of a ionized order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100024 ! calcium cation assay [Term] id: OBI:2100183 name: vented blood gas arterial blood bicarbonate assay def: "An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a vented blood gas order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100043 ! hydrogencarbonate assay [Term] id: OBI:2100184 name: vented blood gas arterial blood oxygen assay def: "An analyte assay that measures the abundance of oxygen in arterial blood as part of a vented blood gas order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100036 ! elemental oxygen assay [Term] id: OBI:2100185 name: vented blood gas arterial blood carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a vented blood gas order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100001 ! carbon dioxide assay [Term] @@ -29080,17 +29224,20 @@ id: OBI:2100186 name: arterial blood hematocrit assay def: "A cytometry assay that measures the proportion of red blood cells in arterial blood" [] is_a: OBI:0003018 ! hematocrit assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100187 name: arterial blood chloride assay def: "An analyte assay that measures the abundance of chloride in arterial blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100010 ! chloride assay [Term] id: OBI:2100188 name: arterial blood hemoglobin assay def: "An analyte assay that measures the abundance of hemoglobin in arterial blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100014 ! hemoglobin assay [Term] @@ -29098,71 +29245,83 @@ id: OBI:2100189 name: GEM premier blood gas venous blood hematocrit assay def: "A cytometry assay that measures the proportion of red blood cells in venous blood as part of a GEM premier blood gas order" [] is_a: OBI:0003018 ! hematocrit assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100190 name: GEM premier blood gas venous blood ionized calcium assay def: "An analyte assay that measures the abundance of ionized calcium in venous blood as part of a GEM premier blood gas order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100024 ! calcium cation assay [Term] id: OBI:2100191 name: GEM premier blood gas venous blood potassium assay def: "An analyte assay that measures the abundance of potassium in venous blood as part of a GEM premier blood gas order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100004 ! potassium(1+) assay [Term] id: OBI:2100192 name: GEM premier blood gas venous blood oxygen assay def: "An analyte assay that measures the abundance of oxygen in venous blood as part of a GEM premier blood gas order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100036 ! elemental oxygen assay [Term] id: OBI:2100193 name: GEM premier blood gas venous blood hemoglobin assay def: "An analyte assay that measures the abundance of hemoglobin in venous blood as part of a GEM premier blood gas order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100014 ! hemoglobin assay [Term] id: OBI:2100194 name: GEM premier blood gas venous blood bicarbonate assay def: "An analyte assay that measures the abundance of bicarbonate in venous blood as part of a GEM premier blood gas order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100043 ! hydrogencarbonate assay [Term] id: OBI:2100195 name: GEM premier blood gas venous blood glucose assay def: "An analyte assay that measures the abundance of glucose in venous blood as part of a GEM premier blood gas order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100020 ! glucose assay [Term] id: OBI:2100196 name: GEM premier blood gas venous blood sodium assay def: "An analyte assay that measures the abundance of sodium in venous blood as part of a GEM premier blood gas order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100002 ! sodium(1+) assay [Term] id: OBI:2100197 name: GEM premier blood gas venous blood lactic acid assay def: "An assay that measures lactic acid in venous blood as part of a GEM premier blood gas order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100042 ! rac-lactic acid assay [Term] id: OBI:2100198 name: GEM premier blood gas venous blood carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a GEM premier blood gas order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100001 ! carbon dioxide assay [Term] id: OBI:2100199 name: trough venous blood tobramycin assay def: "An analyte assay that measures the abundance of tobramycin in venous blood as part of a trough order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100045 ! tobramycin assay [Term] id: OBI:2100200 name: random venous blood tobramycin assay def: "An analyte assay that measures the abundance of tobramycin in venous blood as part of a random order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100045 ! tobramycin assay [Term] @@ -29170,11 +29329,13 @@ id: OBI:2100201 name: CBC with manual differential venous blood metamyelocyte count assay def: "A cytometry assay that measures the count of metamyelocytes in venous blood as part of a CBC with manual differential order" [] is_a: OBI:0003017 ! metamyelocyte assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100202 name: arterial blood lactic acid assay def: "An assay that measures lactic acid in arterial blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100042 ! rac-lactic acid assay [Term] @@ -29182,12 +29343,14 @@ id: OBI:2100203 name: venous blood 25-hydroxyvitamin D2 assay def: "An analyte assay that measures the abundance of 25-hydroxyvitamin D2 in venous blood" [] is_a: OBI:0000443 ! analyte assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100204 name: venous blood digoxin assay def: "An analyte assay that measures the abundance of digoxin in venous blood" [] is_a: OBI:0000443 ! analyte assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100205 @@ -29200,90 +29363,104 @@ is_a: OBI:2100023 ! protein assay id: OBI:2100206 name: venous blood tobramycin assay def: "An analyte assay that measures the abundance of tobramycin in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100045 ! tobramycin assay [Term] id: OBI:2100207 name: CBC with manual differential venous blood myelocyte count assay def: "A cytometry assay that measures the count of myelocytes in venous blood as part of a CBC with manual differential order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:0003165 ! myelocyte count assay [Term] id: OBI:2100208 name: SPEP protein electrophoresis venous blood beta-globin assay def: "An analyte assay that measures the abundance of beta-globin in venous blood as part of a SPEP protein electrophoresis order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100209 name: SPEP protein electrophoresis venous blood albumin assay def: "An analyte assay that measures the abundance of albumin in venous blood as part of a SPEP protein electrophoresis order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100022 ! albumin assay [Term] id: OBI:2100210 name: SPEP protein electrophoresis venous blood protein assay def: "An analyte assay that measures the abundance of protein in venous blood as part of a SPEP protein electrophoresis order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100211 name: trough venous blood vancomycin assay def: "An analyte assay that measures the abundance of vancomycin in venous blood as part of a trough order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100044 ! vancomycin assay [Term] id: OBI:2100212 name: hepatic panel venous blood protein assay def: "An analyte assay that measures the abundance of protein in venous blood as part of a hepatic panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100213 name: hepatic panel venous blood bilirubin assay def: "An analyte assay that measures the abundance of bilirubin in venous blood as part of a hepatic panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100018 ! bilirubin IXalpha assay [Term] id: OBI:2100214 name: hepatic panel venous blood alanine aminotransferase assay def: "An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a hepatic panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100016 ! alanine aminotransferase assay [Term] id: OBI:2100215 name: hepatic panel venous blood human aspartate aminotransferase assay def: "An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a hepatic panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100019 ! aspartate aminotransferase (human) assay [Term] id: OBI:2100216 name: hepatic panel venous blood albumin assay def: "An analyte assay that measures the abundance of albumin in venous blood as part of a hepatic panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100022 ! albumin assay [Term] id: OBI:2100217 name: hepatic panel venous blood human alkaline phosphatase assay def: "An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a hepatic panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100017 ! alkaline phosphatase (human) assay [Term] id: OBI:2100218 name: estimated venous blood glomerular filtration assay def: "An assay that measures glomerular filtration in venous blood as part of a estimated order" [] -is_a: OBI:0000070 ! assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100219 name: DT60 venous blood creatinine assay def: "An analyte assay that measures the abundance of creatinine in venous blood as part of a DT60 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100003 ! creatinine assay [Term] id: OBI:2100220 name: fasting venous blood glucose assay def: "An analyte assay that measures the abundance of glucose in venous blood as part of a fasting order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100020 ! glucose assay [Term] @@ -29291,203 +29468,236 @@ id: OBI:2100221 name: random venous blood amikacin assay def: "An analyte assay that measures the abundance of amikacin in venous blood as part of a random order" [] is_a: OBI:0000443 ! analyte assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100222 name: venous blood ammonia assay def: "An analyte assay that measures the abundance of ammonia in venous blood" [] is_a: OBI:0000443 ! analyte assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100223 name: venous blood GGT assay def: "An analyte assay that measures the abundance of GGT in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100224 name: chem11 venous blood phosphate assay def: "An analyte assay that measures the abundance of phosphate in venous blood as part of a chem11 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100015 ! phosphate ion assay [Term] id: OBI:2100225 name: chem11 venous blood potassium assay def: "An analyte assay that measures the abundance of potassium in venous blood as part of a chem11 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100004 ! potassium(1+) assay [Term] id: OBI:2100226 name: chem11 venous blood calcium assay def: "An analyte assay that measures the abundance of calcium in venous blood as part of a chem11 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100024 ! calcium cation assay [Term] id: OBI:2100227 name: chem11 venous blood glucose assay def: "An analyte assay that measures the abundance of glucose in venous blood as part of a chem11 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100020 ! glucose assay [Term] id: OBI:2100228 name: chem11 venous blood carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a chem11 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100001 ! carbon dioxide assay [Term] id: OBI:2100229 name: chem11 venous blood albumin assay def: "An analyte assay that measures the abundance of albumin in venous blood as part of a chem11 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100022 ! albumin assay [Term] id: OBI:2100230 name: chem11 venous blood sodium assay def: "An analyte assay that measures the abundance of sodium in venous blood as part of a chem11 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100002 ! sodium(1+) assay [Term] id: OBI:2100231 name: chem11 venous blood magnesium assay def: "An analyte assay that measures the abundance of magnesium in venous blood as part of a chem11 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100021 ! magnesium cation assay [Term] id: OBI:2100232 name: chem11 venous blood creatinine assay def: "An analyte assay that measures the abundance of creatinine in venous blood as part of a chem11 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100003 ! creatinine assay [Term] id: OBI:2100233 name: chem11 venous blood chloride assay def: "An analyte assay that measures the abundance of chloride in venous blood as part of a chem11 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100010 ! chloride assay [Term] id: OBI:2100234 name: total venous blood IgE assay def: "An assay that measures IgE in venous blood as part of a total order" [] -is_a: OBI:0000070 ! assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100235 name: chem16 venous blood human aspartate aminotransferase assay def: "An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a chem16 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100019 ! aspartate aminotransferase (human) assay [Term] id: OBI:2100236 name: chem16 venous blood creatinine assay def: "An analyte assay that measures the abundance of creatinine in venous blood as part of a chem16 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100003 ! creatinine assay [Term] id: OBI:2100237 name: chem16 venous blood magnesium assay def: "An analyte assay that measures the abundance of magnesium in venous blood as part of a chem16 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100021 ! magnesium cation assay [Term] id: OBI:2100238 name: chem16 venous blood carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a chem16 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100001 ! carbon dioxide assay [Term] id: OBI:2100239 name: chem16 venous blood glucose assay def: "An analyte assay that measures the abundance of glucose in venous blood as part of a chem16 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100020 ! glucose assay [Term] id: OBI:2100240 name: chem16 venous blood calcium assay def: "An analyte assay that measures the abundance of calcium in venous blood as part of a chem16 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100024 ! calcium cation assay [Term] id: OBI:2100241 name: chem16 venous blood triglyceride assay def: "An analyte assay that measures the abundance of triglyceride in venous blood as part of a chem16 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100029 ! triglyceride assay [Term] id: OBI:2100242 name: chem16 venous blood sodium assay def: "An analyte assay that measures the abundance of sodium in venous blood as part of a chem16 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100002 ! sodium(1+) assay [Term] id: OBI:2100243 name: chem16 venous blood phosphate assay def: "An analyte assay that measures the abundance of phosphate in venous blood as part of a chem16 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100015 ! phosphate ion assay [Term] id: OBI:2100244 name: chem16 venous blood human alkaline phosphatase assay def: "An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a chem16 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100017 ! alkaline phosphatase (human) assay [Term] id: OBI:2100245 name: chem16 venous blood albumin assay def: "An analyte assay that measures the abundance of albumin in venous blood as part of a chem16 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100022 ! albumin assay [Term] id: OBI:2100246 name: chem16 venous blood bilirubin assay def: "An analyte assay that measures the abundance of bilirubin in venous blood as part of a chem16 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100018 ! bilirubin IXalpha assay [Term] id: OBI:2100247 name: chem16 venous blood chloride assay def: "An analyte assay that measures the abundance of chloride in venous blood as part of a chem16 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100010 ! chloride assay [Term] id: OBI:2100248 name: chem16 venous blood alanine aminotransferase assay def: "An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a chem16 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100016 ! alanine aminotransferase assay [Term] id: OBI:2100249 name: chem16 venous blood potassium assay def: "An analyte assay that measures the abundance of potassium in venous blood as part of a chem16 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100004 ! potassium(1+) assay [Term] id: OBI:2100250 name: POC chem8 arterial blood glucose assay def: "An analyte assay that measures the abundance of glucose in arterial blood as part of a POC chem8 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100020 ! glucose assay [Term] id: OBI:2100251 name: POC chem8 arterial blood ionized calcium assay def: "An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a POC chem8 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100024 ! calcium cation assay [Term] id: OBI:2100252 name: POC chem8 arterial blood potassium assay def: "An analyte assay that measures the abundance of potassium in arterial blood as part of a POC chem8 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100004 ! potassium(1+) assay [Term] id: OBI:2100253 name: POC chem8 arterial blood sodium assay def: "An analyte assay that measures the abundance of sodium in arterial blood as part of a POC chem8 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100002 ! sodium(1+) assay [Term] id: OBI:2100254 name: POC chem8 arterial blood creatinine assay def: "An analyte assay that measures the abundance of creatinine in arterial blood as part of a POC chem8 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100003 ! creatinine assay [Term] @@ -29495,17 +29705,20 @@ id: OBI:2100255 name: POC chem8 arterial blood hematocrit assay def: "A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a POC chem8 order" [] is_a: OBI:0003018 ! hematocrit assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100256 name: POC chem8 arterial blood chloride assay def: "An analyte assay that measures the abundance of chloride in arterial blood as part of a POC chem8 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100010 ! chloride assay [Term] id: OBI:2100257 name: peak venous blood tobramycin assay def: "An analyte assay that measures the abundance of tobramycin in venous blood as part of a peak order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100045 ! tobramycin assay [Term] @@ -29519,18 +29732,21 @@ is_a: OBI:2100003 ! creatinine assay id: OBI:2100259 name: intact venous blood PTH assay def: "An analyte assay that measures the abundance of PTH in venous blood as part of a intact order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100034 ! prostate-specific antigen assay [Term] id: OBI:2100260 name: total venous blood PSA assay def: "An analyte assay that measures the abundance of PSA in venous blood as part of a total order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100034 ! prostate-specific antigen assay [Term] id: OBI:2100261 name: total venous blood T3 assay def: "An analyte assay that measures the abundance of T3 in venous blood as part of a total order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100046 ! 3,3',5'-triiodothyronine assay [Term] @@ -29544,12 +29760,14 @@ is_a: OBI:2100023 ! protein assay id: OBI:2100263 name: total venous blood cholesterol assay def: "An analyte assay that measures the abundance of cholesterol in venous blood as part of a total order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100031 ! cholesterol assay [Term] id: OBI:2100264 name: venous blood triglyceride assay def: "An analyte assay that measures the abundance of triglyceride in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100029 ! triglyceride assay [Term] @@ -29585,53 +29803,62 @@ id: OBI:2100269 name: venous blood dehydroepiandrosterone assay def: "An analyte assay that measures the abundance of dehydroepiandrosterone in venous blood" [] is_a: OBI:0000443 ! analyte assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100270 name: venous blood cortisol assay def: "An analyte assay that measures the abundance of cortisol in venous blood" [] is_a: OBI:0000443 ! analyte assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100271 name: ABL90 panel arterial blood sodium assay def: "An analyte assay that measures the abundance of sodium in arterial blood as part of a ABL90 panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100002 ! sodium(1+) assay [Term] id: OBI:2100272 name: ABL90 panel arterial blood oxygen assay def: "An analyte assay that measures the abundance of oxygen in arterial blood as part of a ABL90 panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100036 ! elemental oxygen assay [Term] id: OBI:2100273 name: ABL90 panel arterial blood glucose assay def: "An analyte assay that measures the abundance of glucose in arterial blood as part of a ABL90 panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100020 ! glucose assay [Term] id: OBI:2100274 name: ABL90 panel arterial blood lactic acid assay def: "An assay that measures lactic acid in arterial blood as part of a ABL90 panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100042 ! rac-lactic acid assay [Term] id: OBI:2100275 name: ABL90 panel arterial blood hemoglobin assay def: "An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a ABL90 panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100014 ! hemoglobin assay [Term] id: OBI:2100276 name: ABL90 panel arterial blood chloride assay def: "An analyte assay that measures the abundance of chloride in arterial blood as part of a ABL90 panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100010 ! chloride assay [Term] id: OBI:2100277 name: ABL90 panel arterial blood carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a ABL90 panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100001 ! carbon dioxide assay [Term] @@ -29639,29 +29866,33 @@ id: OBI:2100278 name: ABL90 panel arterial blood hematocrit assay def: "A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a ABL90 panel order" [] is_a: OBI:0003018 ! hematocrit assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100279 name: ABL90 panel arterial blood calcium assay def: "An analyte assay that measures the abundance of calcium in arterial blood as part of a ABL90 panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100024 ! calcium cation assay [Term] id: OBI:2100280 name: ABL90 panel arterial blood temperature assay def: "An assay that measures temperature in arterial blood as part of a ABL90 panel order" [] -is_a: OBI:0000070 ! assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100281 name: ABL90 panel arterial blood bicarbonate assay def: "An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a ABL90 panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100043 ! hydrogencarbonate assay [Term] id: OBI:2100282 name: ABL90 panel arterial blood potassium assay def: "An analyte assay that measures the abundance of potassium in arterial blood as part of a ABL90 panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100004 ! potassium(1+) assay [Term] @@ -29669,29 +29900,34 @@ id: OBI:2100283 name: CBC with manual differential venous blood promyelocyte count assay def: "A cytometry assay that measures the count of promyelocytes in venous blood as part of a CBC with manual differential order" [] is_a: OBI:0003019 ! promyelocyte assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100284 name: ABL90 panel venous blood glucose assay def: "An analyte assay that measures the abundance of glucose in venous blood as part of a ABL90 panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100020 ! glucose assay [Term] id: OBI:2100285 name: ABL90 panel venous blood hemoglobin assay def: "An analyte assay that measures the abundance of hemoglobin in venous blood as part of a ABL90 panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100014 ! hemoglobin assay [Term] id: OBI:2100286 name: ABL90 panel venous blood ionized calcium assay def: "An analyte assay that measures the abundance of ionized calcium in venous blood as part of a ABL90 panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100024 ! calcium cation assay [Term] id: OBI:2100287 name: ABL90 panel venous blood carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a ABL90 panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100001 ! carbon dioxide assay [Term] @@ -29699,53 +29935,62 @@ id: OBI:2100288 name: ABL90 panel venous blood hematocrit assay def: "A cytometry assay that measures the proportion of red blood cells in venous blood as part of a ABL90 panel order" [] is_a: OBI:0003018 ! hematocrit assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100289 name: ABL90 panel venous blood sodium assay def: "An analyte assay that measures the abundance of sodium in venous blood as part of a ABL90 panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100002 ! sodium(1+) assay [Term] id: OBI:2100290 name: ABL90 panel venous blood oxygen assay def: "An analyte assay that measures the abundance of oxygen in venous blood as part of a ABL90 panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100036 ! elemental oxygen assay [Term] id: OBI:2100291 name: ABL90 panel venous blood bicarbonate assay def: "An analyte assay that measures the abundance of bicarbonate in venous blood as part of a ABL90 panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100043 ! hydrogencarbonate assay [Term] id: OBI:2100292 name: ABL90 panel venous blood lactic acid assay def: "An assay that measures lactic acid in venous blood as part of a ABL90 panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100042 ! rac-lactic acid assay [Term] id: OBI:2100293 name: ABL90 panel venous blood chloride assay def: "An analyte assay that measures the abundance of chloride in venous blood as part of a ABL90 panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100010 ! chloride assay [Term] id: OBI:2100294 name: venous blood T4 assay def: "An analyte assay that measures the abundance of T4 in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100035 ! thyroxine assay [Term] id: OBI:2100295 name: free venous blood T4 assay def: "An analyte assay that measures the abundance of T4 in venous blood as part of a free order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100035 ! thyroxine assay [Term] id: OBI:2100296 name: ABL90 panel venous blood potassium assay def: "An analyte assay that measures the abundance of potassium in venous blood as part of a ABL90 panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100004 ! potassium(1+) assay [Term] @@ -29759,48 +30004,56 @@ is_a: OBI:2100002 ! sodium(1+) assay id: OBI:2100298 name: bone profile venous blood albumin assay def: "An analyte assay that measures the abundance of albumin in venous blood as part of a bone profile order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100022 ! albumin assay [Term] id: OBI:2100299 name: bone profile venous blood calcium assay def: "An analyte assay that measures the abundance of calcium in venous blood as part of a bone profile order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100024 ! calcium cation assay [Term] id: OBI:2100300 name: bone profile venous blood human alkaline phosphatase assay def: "An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a bone profile order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100017 ! alkaline phosphatase (human) assay [Term] id: OBI:2100301 name: bone profile venous blood protein assay def: "An analyte assay that measures the abundance of protein in venous blood as part of a bone profile order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100302 name: bone profile venous blood phosphate assay def: "An analyte assay that measures the abundance of phosphate in venous blood as part of a bone profile order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100015 ! phosphate ion assay [Term] id: OBI:2100303 name: ABG/electrolytes arterial blood carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a ABG/electrolytes order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100001 ! carbon dioxide assay [Term] id: OBI:2100304 name: ABG/electrolytes arterial blood oxygen assay def: "An analyte assay that measures the abundance of oxygen in arterial blood as part of a ABG/electrolytes order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100036 ! elemental oxygen assay [Term] id: OBI:2100305 name: ABG/electrolytes arterial blood ionized calcium assay def: "An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a ABG/electrolytes order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100024 ! calcium cation assay [Term] @@ -29808,17 +30061,20 @@ id: OBI:2100306 name: CBC with automated differential venous blood nucleated RBC count assay def: "A cytometry assay that measures the count of nucleated RBCs in venous blood as part of a CBC with automated differential order" [] is_a: OBI:0003018 ! hematocrit assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100307 name: ABL90 panel venous blood methemoglobin assay def: "An analyte assay that measures the abundance of methemoglobin in venous blood as part of a ABL90 panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100040 ! methemoglobin assay [Term] id: OBI:2100308 name: ABL90 panel arterial blood methemoglobin assay def: "An analyte assay that measures the abundance of methemoglobin in arterial blood as part of a ABL90 panel order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100040 ! methemoglobin assay [Term] @@ -29826,29 +30082,34 @@ id: OBI:2100309 name: venous blood valproic acid assay def: "An analyte assay that measures the abundance of valproic acid in venous blood" [] is_a: OBI:0000443 ! analyte assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100310 name: high sensitivity cardiac/neonatal venous blood c-reactive protein assay def: "An analyte assay that measures the abundance of c-reactive protein in venous blood as part of a high sensitivity cardiac/neonatal order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100047 ! C-reactive protein assay [Term] id: OBI:2100311 name: POC arterial blood creatinine assay def: "An analyte assay that measures the abundance of creatinine in arterial blood as part of a POC order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100003 ! creatinine assay [Term] id: OBI:2100312 name: GEM4000 ANLCOOX arterial blood bicarbonate assay def: "An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a GEM4000 ANLCOOX order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100043 ! hydrogencarbonate assay [Term] id: OBI:2100313 name: GEM4000 ANLCOOX arterial blood oxygen assay def: "An analyte assay that measures the abundance of oxygen in arterial blood as part of a GEM4000 ANLCOOX order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100036 ! elemental oxygen assay [Term] @@ -29856,59 +30117,68 @@ id: OBI:2100314 name: GEM4000 ANLCOOX arterial blood hematocrit assay def: "A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a GEM4000 ANLCOOX order" [] is_a: OBI:0003018 ! hematocrit assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100315 name: GEM4000 ANLCOOX arterial blood temperature assay def: "An assay that measures temperature in arterial blood as part of a GEM4000 ANLCOOX order" [] -is_a: OBI:0000070 ! assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100316 name: GEM4000 ANLCOOX arterial blood hemoglobin assay def: "An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a GEM4000 ANLCOOX order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100014 ! hemoglobin assay [Term] id: OBI:2100317 name: GEM4000 ANLCOOX arterial blood potassium assay def: "An analyte assay that measures the abundance of potassium in arterial blood as part of a GEM4000 ANLCOOX order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100004 ! potassium(1+) assay [Term] id: OBI:2100318 name: GEM4000 ANLCOOX arterial blood glucose assay def: "An analyte assay that measures the abundance of glucose in arterial blood as part of a GEM4000 ANLCOOX order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100020 ! glucose assay [Term] id: OBI:2100319 name: GEM4000 ANLCOOX arterial blood ionized calcium assay def: "An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a GEM4000 ANLCOOX order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100024 ! calcium cation assay [Term] id: OBI:2100320 name: GEM4000 ANLCOOX arterial blood carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a GEM4000 ANLCOOX order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100001 ! carbon dioxide assay [Term] id: OBI:2100321 name: GEM4000 ANLCOOX arterial blood sodium assay def: "An analyte assay that measures the abundance of sodium in arterial blood as part of a GEM4000 ANLCOOX order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100002 ! sodium(1+) assay [Term] id: OBI:2100322 name: ionized venous blood calcium assay def: "An analyte assay that measures the abundance of calcium in venous blood as part of a ionized order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100024 ! calcium cation assay [Term] id: OBI:2100323 name: venous blood hemoglobin assay def: "An analyte assay that measures the abundance of hemoglobin in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100014 ! hemoglobin assay [Term] @@ -29916,23 +30186,27 @@ id: OBI:2100324 name: CBC with manual differential venous blood megakaryocyte count assay def: "A cytometry assay that measures the count of megakaryocytes in venous blood as part of a CBC with manual differential order" [] is_a: OBI:0001977 ! cytometry assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100325 name: non-cardiac venous blood c-reactive protein assay def: "An analyte assay that measures the abundance of c-reactive protein in venous blood as part of a non-cardiac order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100047 ! C-reactive protein assay [Term] id: OBI:2100326 name: intraoperative venous blood PTH assay def: "An analyte assay that measures the abundance of PTH in venous blood as part of a intraoperative order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100034 ! prostate-specific antigen assay [Term] id: OBI:2100327 name: venous blood parathyroid hormone assay def: "An analyte assay that measures the abundance of parathyroid hormone in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100023 ! protein assay [Term] @@ -29999,42 +30273,49 @@ is_a: OBI:0003023 ! eosinophil assay id: OBI:2100338 name: liver function venous blood bilirubin assay def: "An analyte assay that measures the abundance of bilirubin in venous blood as part of a liver function order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100018 ! bilirubin IXalpha assay [Term] id: OBI:2100339 name: liver function venous blood alanine aminotransferase assay def: "An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a liver function order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100016 ! alanine aminotransferase assay [Term] id: OBI:2100340 name: liver function venous blood human aspartate aminotransferase assay def: "An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver function order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100019 ! aspartate aminotransferase (human) assay [Term] id: OBI:2100341 name: liver function venous blood albumin assay def: "An analyte assay that measures the abundance of albumin in venous blood as part of a liver function order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100022 ! albumin assay [Term] id: OBI:2100342 name: liver function venous blood protein assay def: "An analyte assay that measures the abundance of protein in venous blood as part of a liver function order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100343 name: liver function venous blood human alkaline phosphatase assay def: "An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a liver function order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100017 ! alkaline phosphatase (human) assay [Term] id: OBI:2100344 name: vitamin B12 and Folate venous blood folic acid assay def: "An analyte assay that measures the abundance of folic acid in venous blood as part of a vitamin B12 and Folate order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100037 ! folic acids assay [Term] @@ -30048,6 +30329,7 @@ id: OBI:2100346 name: venous blood reticulocyte count assay def: "A cytometry assay that measures the count of reticulocytes in venous blood" [] is_a: OBI:0003026 ! reticulocyte assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100347 @@ -30059,18 +30341,21 @@ is_a: OBI:2100031 ! cholesterol assay id: OBI:2100348 name: TSH reflex Free T4 venous blood thyroid stimulating hormone assay def: "An analyte assay that measures the abundance of thyroid stimulating hormone in venous blood as part of a TSH reflex Free T4 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100033 ! thyroid stimulating hormone assay [Term] id: OBI:2100349 name: direct venous blood bilirubin assay def: "An analyte assay that measures the abundance of bilirubin in venous blood as part of a direct order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100018 ! bilirubin IXalpha assay [Term] id: OBI:2100350 name: free venous blood T3 assay def: "An analyte assay that measures the abundance of T3 in venous blood as part of a free order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100046 ! 3,3',5'-triiodothyronine assay [Term] @@ -30090,41 +30375,47 @@ id: OBI:2100353 name: hemoglobin and hematocrit venous blood hematocrit assay def: "A cytometry assay that measures the proportion of red blood cells in venous blood as part of a hemoglobin and hematocrit order" [] is_a: OBI:0003018 ! hematocrit assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100354 name: hemoglobin and hematocrit venous blood hemoglobin assay def: "An analyte assay that measures the abundance of hemoglobin in venous blood as part of a hemoglobin and hematocrit order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100014 ! hemoglobin assay [Term] id: OBI:2100355 name: venous blood ionized calcium assay def: "An analyte assay that measures the abundance of ionized calcium in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100024 ! calcium cation assay [Term] id: OBI:2100356 name: venous blood temperature assay def: "An assay that measures temperature in venous blood" [] -is_a: OBI:0000070 ! assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100357 name: venous blood bicarbonate assay def: "An analyte assay that measures the abundance of bicarbonate in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100043 ! hydrogencarbonate assay [Term] id: OBI:2100358 name: venous blood oxygen assay def: "An analyte assay that measures the abundance of oxygen in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100036 ! elemental oxygen assay [Term] id: OBI:2100359 name: venous blood osmolality assay def: "An assay that measures osmolality in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100039 ! osmolality assay [Term] @@ -30132,11 +30423,13 @@ id: OBI:2100360 name: liver fibrosis (chronic viral hepatitis) venous blood platelet count assay def: "A cytometry assay that measures the count of platelets in venous blood as part of a liver fibrosis (chronic viral hepatitis) order" [] is_a: OBI:0003028 ! platelet assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100361 name: venous blood T3 assay def: "An analyte assay that measures the abundance of T3 in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100046 ! 3,3',5'-triiodothyronine assay [Term] @@ -30144,6 +30437,7 @@ id: OBI:2100362 name: CBC with manual differential venous blood neutrophil count assay def: "A cytometry assay that measures the count of neutrophils in venous blood as part of a CBC with manual differential order" [] is_a: OBI:0003022 ! neutrophil assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100363 @@ -30156,6 +30450,7 @@ is_a: OBI:2100003 ! creatinine assay id: OBI:2100364 name: venous blood beta hydroxybutryic acid assay def: "An analyte assay that measures the abundance of beta hydroxybutryic acid in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100051 ! 3-hydroxybutyric acid assay [Term] @@ -30163,83 +30458,96 @@ id: OBI:2100365 name: venous blood megakaryocyte count assay def: "A cytometry assay that measures the count of megakaryocytes in venous blood" [] is_a: OBI:0001977 ! cytometry assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100366 name: venous blood nucleated RBC count assay def: "A cytometry assay that measures the count of nucleated RBCs in venous blood" [] is_a: OBI:0003018 ! hematocrit assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100367 name: venous blood WBC count assay def: "A cytometry assay that measures the count of WBCs in venous blood" [] is_a: OBI:0001977 ! cytometry assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100368 name: automated count venous blood reticulocyte count assay def: "A cytometry assay that measures the count of reticulocytes in venous blood as part of a automated count order" [] is_a: OBI:0003026 ! reticulocyte assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100369 name: total venous blood homocysteine assay def: "An analyte assay that measures the abundance of homocysteine in venous blood as part of a total order" [] is_a: OBI:0000443 ! analyte assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100370 name: venous blood Ceruloplasmin assay def: "An analyte assay that measures the abundance of Ceruloplasmin in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100371 name: GEM4 arterial blood bicarbonate assay def: "An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a GEM4 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100043 ! hydrogencarbonate assay [Term] id: OBI:2100372 name: GEM4 arterial blood lactic acid assay def: "An assay that measures lactic acid in arterial blood as part of a GEM4 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100042 ! rac-lactic acid assay [Term] id: OBI:2100373 name: GEM4 arterial blood hemoglobin assay def: "An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a GEM4 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100014 ! hemoglobin assay [Term] id: OBI:2100374 name: GEM4 arterial blood sodium assay def: "An analyte assay that measures the abundance of sodium in arterial blood as part of a GEM4 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100002 ! sodium(1+) assay [Term] id: OBI:2100375 name: GEM4 arterial blood potassium assay def: "An analyte assay that measures the abundance of potassium in arterial blood as part of a GEM4 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100004 ! potassium(1+) assay [Term] id: OBI:2100376 name: GEM4 arterial blood temperature assay def: "An assay that measures temperature in arterial blood as part of a GEM4 order" [] -is_a: OBI:0000070 ! assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100377 name: GEM4 arterial blood glucose assay def: "An analyte assay that measures the abundance of glucose in arterial blood as part of a GEM4 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100020 ! glucose assay [Term] id: OBI:2100378 name: GEM4 arterial blood oxygen assay def: "An analyte assay that measures the abundance of oxygen in arterial blood as part of a GEM4 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100036 ! elemental oxygen assay [Term] @@ -30247,17 +30555,20 @@ id: OBI:2100379 name: GEM4 arterial blood hematocrit assay def: "A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a GEM4 order" [] is_a: OBI:0003018 ! hematocrit assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100380 name: GEM4 arterial blood ionized calcium assay def: "An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a GEM4 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100024 ! calcium cation assay [Term] id: OBI:2100381 name: GEM4 arterial blood carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a GEM4 order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100001 ! carbon dioxide assay [Term] @@ -30265,11 +30576,13 @@ id: OBI:2100382 name: liver fibrosis (NAFLD) venous blood platelet count assay def: "A cytometry assay that measures the count of platelets in venous blood as part of a liver fibrosis (NAFLD) order" [] is_a: OBI:0003028 ! platelet assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100383 name: venous blood beta hydroxybutric acid assay def: "An analyte assay that measures the abundance of beta hydroxybutric acid in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100051 ! 3-hydroxybutyric acid assay [Term] @@ -30277,35 +30590,41 @@ id: OBI:2100384 name: CBC with manual differential venous blood plasma cell count assay def: "A cytometry assay that measures the count of plasma cells in venous blood as part of a CBC with manual differential order" [] is_a: OBI:0003024 ! lymphocyte assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:2100385 name: venous blood erythropoietin assay def: "An analyte assay that measures the abundance of erythropoietin in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100386 name: blood gas arterial blood oxygen assay def: "An analyte assay that measures the abundance of oxygen in arterial blood as part of a blood gas order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100036 ! elemental oxygen assay [Term] id: OBI:2100387 name: blood gas arterial blood bicarbonate assay def: "An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a blood gas order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100043 ! hydrogencarbonate assay [Term] id: OBI:2100388 name: blood gas arterial blood carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a blood gas order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100001 ! carbon dioxide assay [Term] id: OBI:2100389 name: free/total venous blood PSA assay def: "An analyte assay that measures the abundance of PSA in venous blood as part of a free/total order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100034 ! prostate-specific antigen assay [Term] @@ -30361,30 +30680,35 @@ is_a: OBI:0003232 ! cerebrospinal fluid assay id: OBI:2100397 name: venous blood beta-2-microglobulin assay def: "An analyte assay that measures the abundance of beta-2-microglobulin in venous blood" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100398 name: lipid panel reflex direct venous blood low density lipoprotein assay def: "An analyte assay that measures the abundance of low density lipoprotein in venous blood as part of a Lipid panel reflex direct order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100032 ! low-density lipoprotein cholesterol assay [Term] id: OBI:2100399 name: lipid panel reflex direct venous blood triglyceride assay def: "An analyte assay that measures the abundance of triglyceride in venous blood as part of a Lipid panel reflex direct order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100029 ! triglyceride assay [Term] id: OBI:2100400 name: lipid panel reflex direct venous blood cholesterol assay def: "An analyte assay that measures the abundance of cholesterol in venous blood as part of a Lipid panel reflex direct order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100031 ! cholesterol assay [Term] id: OBI:2100401 name: lipid panel reflex direct venous blood high density lipoprotein assay def: "An analyte assay that measures the abundance of high density lipoprotein in venous blood as part of a Lipid panel reflex direct order" [] +is_a: OBI:0003040 ! blood assay is_a: OBI:2100030 ! high-density lipoprotein cholesterol assay [Term] @@ -31300,6 +31624,12 @@ name: life cycle stage def: "A spatiotemporal region encompassing some part of the life cycle of an organism." [] is_a: GO:0008150 ! biological_process +[Term] +id: UBERON:0000162 +name: cloaca +def: "Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures." [] +is_a: UBERON:0000465 ! material anatomical entity + [Term] id: UBERON:0000165 name: mouth diff --git a/views/obi_core.owl b/views/obi_core.owl index 03bd7c4e..a2b387e6 100644 --- a/views/obi_core.owl +++ b/views/obi_core.owl @@ -11,7 +11,7 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"> - + en Ontology for Biomedical Investigations Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester @@ -78,7 +78,7 @@ http://creativecommons.org/licenses/by/4.0/ Ontology for Biomedical Investigations Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2024-10-25 + 2024-12-05 @@ -2658,7 +2658,7 @@ editor = PRS specimen role liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient. - a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation + A role borne by a material entity that is obtained during a specimen collection process and that can be realized by performing measurements or observations on the specimen. 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. blood taken from animal: animal continues in study, whereas blood has role specimen. @@ -3046,9 +3046,10 @@ for now. specimen collection process - drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation + drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation, collecting a stone from a site - A planned process with the objective of collecting a specimen. + A planned process with the objective to obtain a material entity for potential use as an input upon which measurements or observations are performed. + Definition updated following discussion on 2024-10-07 OBI dev call. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. Philly2013: The specimen_role for the specimen is created during the specimen collection process. @@ -3070,7 +3071,8 @@ http://sourceforge.net/p/obi/obi-terms/716/ specimen collection objective The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. - A objective specification to obtain a material entity for potential use as an input during an investigation. + A objective specification that is fulfilled by obtaining a material entity for potential use as an input upon which measurements or observations are performed. + OBI recommends against subclassing this term in order to avoid further parallel hierarchies between this term and specimen collection process. Bjoern Peters Bjoern Peters specimen collection objective @@ -3226,21 +3228,24 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + + + + + + processed specimen - A tissue sample that has been sliced and stained for a histology study. -A blood specimen that has been centrifuged to obtain the white blood cells. A specimen that has been intentionally physically modified. + A tissue sample that has been sliced and stained for a histology study. Bjoern Peters Bjoern Peters - A tissue sample that has been sliced and stained for a histology study. processed specimen @@ -3297,6 +3302,76 @@ In the examples above, a reagent is an operational component of a device, but th + + + + + + + + + + + + + + + + cell specimen + + A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture. + Discussed on obi call Jan 23, 2017. To improve cell specimen that include single cell specimen. Details see tracker: https://sourceforge.net/p/obi/obi-terms/828 + PERSON: Chris Stoeckert, Jie Zheng, Alexander Diehl + MO_612 cell + cell specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + specimen from organism + + A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm). + PERSON: Chris Stoeckert, Jie Zheng + tissue specimen + MO_954 organism_part + specimen from organism + + + + @@ -3605,10 +3680,9 @@ This issue is outside the scope of OBI. specimen - Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. + Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen; collecting a stone from a site. - A material entity that has the specimen role. - Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. + A material entity that is collected for potential use as an input upon which measurements or observations are performed. PERSON: James Malone PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch @@ -3938,6 +4012,30 @@ realizes some 'host of immune response role' + + + + + material anatomical entity + Anatomical entity that has mass. + + material anatomical entity + + + + + + + + + anatomical cluster + Anatomical group whose component anatomical structures lie in close proximity to each other. + + anatomical cluster + + + +