-
-
Notifications
You must be signed in to change notification settings - Fork 21
Home
Rintze M. Zelle edited this page Oct 22, 2016
·
5 revisions
This page provides background information on how Reference Extractor extracts item metadata from Word documents. Both Zotero and Mendeley (optionally) embed item metadata in Word documents within the citation fields as field codes. Within .docx files (which are basically just zipped files), these field codes can be found in the word/document.xml file. Each field code is wrapped in an <w:instrText/> element.
Below are some examples of how Zotero and Mendeley embed item metadata in these fields.
Examples generated with Zotero 4.0.29.10.
Full field:
<w:instrText xml:space="preserve"> ADDIN ZOTERO_ITEM CSL_CITATION {"citationID":"2lou5a94nk","properties":{"formattedCitation":"(Zelle, Shaw, & van Dijken, 2014)","plainCitation":"(Zelle, Shaw, & van Dijken, 2014)"},"citationItems":[{"id":255,"uris":["http://zotero.org/users/1031436/items/TVJVND6G"],"uri":["http://zotero.org/users/1031436/items/TVJVND6G"],"itemData":{"id":255,"type":"patent","title":"Method for acetate consumption during ethanolic fermentation of cellulosic feedstocks","abstract":"The present invention provides for novel metabolic pathways to detoxify biomass- derived acetate via metabolic conversion to ethanol, acetone, or isopropanol. More specifically, the invention provides for a recombinant microorganism comprising one or more native and/or heterologous enzymes that function in one or more first engineered metabolic pathways to achieve: (1) conversion of acetate to ethanol; (2) conversion of acetate to acetone; or (3) conversion of acetate to isopropanol; and one or more native and/or heterologous enzymes that function in one or more second engineered metabolic pathways to produce an electron donor used in the conversion of acetate to less inhibitory compounds; wherein the one or more native and/or heterologous enzymes is activated, upregulated, or downregulated., La présente invention concerne de nouvelles voies métaboliques pour détoxifier de l'acétate dérivé d'une biomasse par conversion métabolique en éthanol, acétone ou isopropanol. Plus spécifiquement, l'invention concerne un microorganisme recombiné comprenant une ou plusieurs enzymes natives et/ou hétérologues qui fonctionnent dans une ou plusieurs premières voies métaboliques modifiées pour permettre : (1) la conversion de l'acétate en éthanol; (2) la conversion de l'acétate en acétone; ou (3) la conversion de l'acétate en isopropanol; et une ou plusieurs enzymes natives et/ou hétérologues qui fonctionnent dans une ou plusieurs secondes voies métaboliques modifiées pour produire un donneur d'électrons utilisé dans la conversion de l'acétate en composés moins inhibiteurs, la ou les enzymes natives et/ou hétérologues étant activées, positivement régulées ou négativement régulées.","URL":"https://patentscope.wipo.int/search/en/WO2014074895","call-number":"PCT/US2013/069266","number":"WO2014074895","language":"English (EN)","author":[{"family":"Zelle","given":"Rintze Meindert"},{"family":"Shaw","given":"Arthur J."},{"family":"Dijken","given":"Johannes Pieter","non-dropping-particle":"van"}],"issued":{"date-parts":[["2014",5,16]]},"accessed":{"date-parts":[["2014",7,13]]}}}],"schema":"https://github.com/citation-style-language/schema/raw/master/csl-citation.json"} </w:instrText>
Reindented JSON:
{
"citationID": "2lou5a94nk",
"properties": {
"formattedCitation": "(Zelle, Shaw, & van Dijken, 2014)",
"plainCitation": "(Zelle, Shaw, & van Dijken, 2014)"
},
"citationItems": [{
"id": 255,
"uris": ["http://zotero.org/users/1031436/items/TVJVND6G"],
"uri": ["http://zotero.org/users/1031436/items/TVJVND6G"],
"itemData": {
"id": 255,
"type": "patent",
"title": "Method for acetate consumption during ethanolic fermentation of cellulosic feedstocks",
"abstract": "The present invention provides for novel metabolic pathways to detoxify biomass- derived acetate via metabolic conversion to ethanol, acetone, or isopropanol. More specifically, the invention provides for a recombinant microorganism comprising one or more native and/or heterologous enzymes that function in one or more first engineered metabolic pathways to achieve: (1) conversion of acetate to ethanol; (2) conversion of acetate to acetone; or (3) conversion of acetate to isopropanol; and one or more native and/or heterologous enzymes that function in one or more second engineered metabolic pathways to produce an electron donor used in the conversion of acetate to less inhibitory compounds; wherein the one or more native and/or heterologous enzymes is activated, upregulated, or downregulated., La présente invention concerne de nouvelles voies métaboliques pour détoxifier de l'acétate dérivé d'une biomasse par conversion métabolique en éthanol, acétone ou isopropanol. Plus spécifiquement, l'invention concerne un microorganisme recombiné comprenant une ou plusieurs enzymes natives et/ou hétérologues qui fonctionnent dans une ou plusieurs premières voies métaboliques modifiées pour permettre : (1) la conversion de l'acétate en éthanol; (2) la conversion de l'acétate en acétone; ou (3) la conversion de l'acétate en isopropanol; et une ou plusieurs enzymes natives et/ou hétérologues qui fonctionnent dans une ou plusieurs secondes voies métaboliques modifiées pour produire un donneur d'électrons utilisé dans la conversion de l'acétate en composés moins inhibiteurs, la ou les enzymes natives et/ou hétérologues étant activées, positivement régulées ou négativement régulées.",
"URL": "https://patentscope.wipo.int/search/en/WO2014074895",
"call-number": "PCT/US2013/069266",
"number": "WO2014074895",
"language": "English (EN)",
"author": [{
"family": "Zelle",
"given": "Rintze Meindert"
}, {
"family": "Shaw",
"given": "Arthur J."
}, {
"family": "Dijken",
"given": "Johannes Pieter",
"non-dropping-particle": "van"
}],
"issued": {
"date-parts": [
["2014", 5, 16]
]
},
"accessed": {
"date-parts": [
["2014", 7, 13]
]
}
}
}],
"schema": "https://github.com/citation-style-language/schema/raw/master/csl-citation.json"
}Full field:
<w:instrText xml:space="preserve"> ADDIN ZOTERO_ITEM CSL_CITATION {"citationID":"2e69rb87ph","properties":{"formattedCitation":"(Abbott, Zelle, Pronk, & Van Maris, 2009; Henningsen et al., 2015)","plainCitation":"(Abbott, Zelle, Pronk, & Van Maris, 2009; Henningsen et al., 2015)"},"citationItems":[{"id":223,"uris":["http://zotero.org/users/1031436/items/RWDHMJ3F"],"uri":["http://zotero.org/users/1031436/items/RWDHMJ3F"],"itemData":{"id":223,"type":"article-journal","title":"Metabolic engineering of Saccharomyces cerevisiae for production of carboxylic acids: current status and challenges","container-title":"FEMS Yeast Research","page":"1123–1136","volume":"9","issue":"8","source":"Wiley Online Library","abstract":"To meet the demands of future generations for chemicals and energy and to reduce the environmental footprint of the chemical industry, alternatives for petrochemistry are required. Microbial conversion of renewable feedstocks has a huge potential for cleaner, sustainable industrial production of fuels and chemicals. Microbial production of organic acids is a promising approach for production of chemical building blocks that can replace their petrochemically derived equivalents. Although Saccharomyces cerevisiae does not naturally produce organic acids in large quantities, its robustness, pH tolerance, simple nutrient requirements and long history as an industrial workhorse make it an excellent candidate biocatalyst for such processes. Genetic engineering, along with evolution and selection, has been successfully used to divert carbon from ethanol, the natural endproduct of S. cerevisiae, to pyruvate. Further engineering, which included expression of heterologous enzymes and transporters, yielded strains capable of producing lactate and malate from pyruvate. Besides these metabolic engineering strategies, this review discusses the impact of transport and energetics as well as the tolerance towards these organic acids. In addition to recent progress in engineering S. cerevisiae for organic acid production, the key limitations and challenges are discussed in the context of sustainable industrial production of organic acids from renewable feedstocks.","URL":"http://onlinelibrary.wiley.com/doi/10.1111/j.1567-1364.2009.00537.x/abstract","DOI":"10.1111/j.1567-1364.2009.00537.x","ISSN":"1567-1364","shortTitle":"Metabolic engineering of Saccharomyces cerevisiae for production of carboxylic acids","language":"en","author":[{"family":"Abbott","given":"Derek A."},{"family":"Zelle","given":"Rintze M."},{"family":"Pronk","given":"Jack T."},{"family":"Van Maris","given":"Antonius J.A."}],"issued":{"date-parts":[["2009"]]},"accessed":{"date-parts":[["2012",7,13]]}}},{"id":1249,"uris":["http://zotero.org/users/1031436/items/AWBCXKXR"],"uri":["http://zotero.org/users/1031436/items/AWBCXKXR"],"itemData":{"id":1249,"type":"article-journal","title":"Increasing anaerobic acetate consumption and ethanol yield in Saccharomyces cerevisiae with NADPH-specific alcohol dehydrogenase","container-title":"Applied and Environmental Microbiology","source":"PubMed","abstract":"Saccharomyces cerevisiae has recently been engineered to use acetate, a primary inhibitor in lignocellulosic hydrolysates, as co-substrate during anaerobic ethanolic fermentation. However, the original metabolic pathway devised to convert acetate to ethanol uses NADH-specific acetylating acetaldehyde dehydrogenase and alcohol dehydrogenase, and quickly becomes constrained by limited NADH availability, even when glycerol formation is abolished.We present alcohol dehydrogenase as a novel target for anaerobic redox engineering of S. cerevisiae. Introduction of an NADPH-specific alcohol dehydrogenase not only reduces the NADH demand of the acetate-to-ethanol pathway, but also allows the cell to effectively exchange NADPH for NADH during sugar fermentation. Unlike NADH, NADPH can be freely generated under anaerobic conditions, via the oxidative pentose phosphate pathway.We show that an industrial bioethanol strain engineered with the original pathway (expressing acetylating acetaldehyde dehydrogenase from Bifidobacterium adolescentis and with deletions of glycerol-3-phosphate dehydrogenases GPD1 and GPD2) consumed 1.9 g l(-1) acetate during fermentation of 114 g l(-1) glucose. Combined with a decrease in glycerol production from 4.0 to 0.1 g l(-1), this increased the ethanol yield by 4% over the wild type. We provide evidence that acetate consumption in this strain is indeed limited by NADH availability. By introducing an NADPH-ADH from Entamoeba histolytica and overexpressing ACS2 and ZWF1, we increased acetate consumption to 5.3 g l(-1) and raised the ethanol yield to 7% above the wild-type level.","DOI":"10.1128/AEM.01689-15","ISSN":"1098-5336","note":"PMID: 26386051","journalAbbreviation":"Appl. Environ. Microbiol.","language":"ENG","author":[{"family":"Henningsen","given":"Brooks M."},{"family":"Hon","given":"Shuen"},{"family":"Covalla","given":"Sean F."},{"family":"Sonu","given":"Carolina"},{"family":"Argyros","given":"D. Aaron"},{"family":"Barrett","given":"Trisha F."},{"family":"Wiswall","given":"Erin"},{"family":"Froehlich","given":"Allan C."},{"family":"Zelle","given":"Rintze M."}],"issued":{"date-parts":[["2015",9,18]]},"PMID":"26386051"}}],"schema":"https://github.com/citation-style-language/schema/raw/master/csl-citation.json"} </w:instrText>
Reindented JSON:
{
"citationID": "2e69rb87ph",
"properties": {
"formattedCitation": "(Abbott, Zelle, Pronk, & Van Maris, 2009; Henningsen et al., 2015)",
"plainCitation": "(Abbott, Zelle, Pronk, & Van Maris, 2009; Henningsen et al., 2015)"
},
"citationItems": [{
"id": 223,
"uris": ["http://zotero.org/users/1031436/items/RWDHMJ3F"],
"uri": ["http://zotero.org/users/1031436/items/RWDHMJ3F"],
"itemData": {
"id": 223,
"type": "article-journal",
"title": "Metabolic engineering of Saccharomyces cerevisiae for production of carboxylic acids: current status and challenges",
"container-title": "FEMS Yeast Research",
"page": "1123–1136",
"volume": "9",
"issue": "8",
"source": "Wiley Online Library",
"abstract": "To meet the demands of future generations for chemicals and energy and to reduce the environmental footprint of the chemical industry, alternatives for petrochemistry are required. Microbial conversion of renewable feedstocks has a huge potential for cleaner, sustainable industrial production of fuels and chemicals. Microbial production of organic acids is a promising approach for production of chemical building blocks that can replace their petrochemically derived equivalents. Although Saccharomyces cerevisiae does not naturally produce organic acids in large quantities, its robustness, pH tolerance, simple nutrient requirements and long history as an industrial workhorse make it an excellent candidate biocatalyst for such processes. Genetic engineering, along with evolution and selection, has been successfully used to divert carbon from ethanol, the natural endproduct of S. cerevisiae, to pyruvate. Further engineering, which included expression of heterologous enzymes and transporters, yielded strains capable of producing lactate and malate from pyruvate. Besides these metabolic engineering strategies, this review discusses the impact of transport and energetics as well as the tolerance towards these organic acids. In addition to recent progress in engineering S. cerevisiae for organic acid production, the key limitations and challenges are discussed in the context of sustainable industrial production of organic acids from renewable feedstocks.",
"URL": "http://onlinelibrary.wiley.com/doi/10.1111/j.1567-1364.2009.00537.x/abstract",
"DOI": "10.1111/j.1567-1364.2009.00537.x",
"ISSN": "1567-1364",
"shortTitle": "Metabolic engineering of Saccharomyces cerevisiae for production of carboxylic acids",
"language": "en",
"author": [{
"family": "Abbott",
"given": "Derek A."
}, {
"family": "Zelle",
"given": "Rintze M."
}, {
"family": "Pronk",
"given": "Jack T."
}, {
"family": "Van Maris",
"given": "Antonius J.A."
}],
"issued": {
"date-parts": [
["2009"]
]
},
"accessed": {
"date-parts": [
["2012", 7, 13]
]
}
}
}, {
"id": 1249,
"uris": ["http://zotero.org/users/1031436/items/AWBCXKXR"],
"uri": ["http://zotero.org/users/1031436/items/AWBCXKXR"],
"itemData": {
"id": 1249,
"type": "article-journal",
"title": "Increasing anaerobic acetate consumption and ethanol yield in Saccharomyces cerevisiae with NADPH-specific alcohol dehydrogenase",
"container-title": "Applied and Environmental Microbiology",
"source": "PubMed",
"abstract": "Saccharomyces cerevisiae has recently been engineered to use acetate, a primary inhibitor in lignocellulosic hydrolysates, as co-substrate during anaerobic ethanolic fermentation. However, the original metabolic pathway devised to convert acetate to ethanol uses NADH-specific acetylating acetaldehyde dehydrogenase and alcohol dehydrogenase, and quickly becomes constrained by limited NADH availability, even when glycerol formation is abolished.We present alcohol dehydrogenase as a novel target for anaerobic redox engineering of S. cerevisiae. Introduction of an NADPH-specific alcohol dehydrogenase not only reduces the NADH demand of the acetate-to-ethanol pathway, but also allows the cell to effectively exchange NADPH for NADH during sugar fermentation. Unlike NADH, NADPH can be freely generated under anaerobic conditions, via the oxidative pentose phosphate pathway.We show that an industrial bioethanol strain engineered with the original pathway (expressing acetylating acetaldehyde dehydrogenase from Bifidobacterium adolescentis and with deletions of glycerol-3-phosphate dehydrogenases GPD1 and GPD2) consumed 1.9 g l(-1) acetate during fermentation of 114 g l(-1) glucose. Combined with a decrease in glycerol production from 4.0 to 0.1 g l(-1), this increased the ethanol yield by 4% over the wild type. We provide evidence that acetate consumption in this strain is indeed limited by NADH availability. By introducing an NADPH-ADH from Entamoeba histolytica and overexpressing ACS2 and ZWF1, we increased acetate consumption to 5.3 g l(-1) and raised the ethanol yield to 7% above the wild-type level.",
"DOI": "10.1128/AEM.01689-15",
"ISSN": "1098-5336",
"note": "PMID: 26386051",
"journalAbbreviation": "Appl. Environ. Microbiol.",
"language": "ENG",
"author": [{
"family": "Henningsen",
"given": "Brooks M."
}, {
"family": "Hon",
"given": "Shuen"
}, {
"family": "Covalla",
"given": "Sean F."
}, {
"family": "Sonu",
"given": "Carolina"
}, {
"family": "Argyros",
"given": "D. Aaron"
}, {
"family": "Barrett",
"given": "Trisha F."
}, {
"family": "Wiswall",
"given": "Erin"
}, {
"family": "Froehlich",
"given": "Allan C."
}, {
"family": "Zelle",
"given": "Rintze M."
}],
"issued": {
"date-parts": [
["2015", 9, 18]
]
},
"PMID": "26386051"
}
}],
"schema": "https://github.com/citation-style-language/schema/raw/master/csl-citation.json"
}Full field:
<w:instrText xml:space="preserve"> ADDIN ZOTERO_BIBL {"uncited":[["http://zotero.org/users/1031436/items/HU4NC489"],["http://zotero.org/users/1031436/items/WZFNPG9D"]],"custom":[]} CSL_BIBLIOGRAPHY </w:instrText>
It seems that, even with the "Store references in Document" option checked, Zotero 4.0.29.10 does not store item metadata within .docx Word documents for so-called 'uncited' items that are added directly to the bibliography via Zotero's "Edit Bibliography" button.