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Support ORCID API identifier types? #365

Open vincerubinetti opened 1 year ago

vincerubinetti commented 1 year ago

ORCID has APIs that can return paper identifiers of the following types: https://pub.orcid.org/v3.0/identifiers

For example, about 10% Casey Greene's papers returned from ORCID don't have a doi, but instead have an eid or wosuid or others. It'd be nice if Manubot could support citing such papers.

ORCID unfortunately seems to provide very little info about what these identifiers are or where they come from. For example, is eid the same as civic.eid here...

Not sure if this is doable with upstream packages/services.

dhimmel commented 1 year ago

Can you provide the identifiers as well for a wosid, eid, and source-work-id (particularly the records without a DOI)? I'd like to learn more about those works and what's the best way to cite them.

More generally, we rely on Bioregistry for assigning prefixes. In an ideal world, ORCID would align their prefixes with more standard Bioregistry prefixes whenever possible. But in the meantime, perhaps we can define a mapping from ORCID-style prefix to Bioregistry-style prefix which would enable Manubot citation support.

I think wosid is Web of Science ID. Bioregistry would likely accept registration of the wosid prefix.

I don't think the ORCID eid prefix is a synonym for civic.eid which refers to Clinical Interpretation of Variants in Cancer.

vincerubinetti commented 1 year ago

Here are a few IDs as examples:

eid:2-s2.0-85012144154
wosuid:WOS:000386326200051
source-work-id:0417180825983-87

And here is the full (JSON, not XML) API response for the ~10% of Casey's papers that don't have a doi (in the top-level external-ids), just in case the extra info gives some clues:

JSON ```json [ { "last-modified-date": { "value": 1653595164746 }, "external-ids": { "external-id": [ { "external-id-type": "eid", "external-id-value": "2-s2.0-85012144154", "external-id-normalized": { "value": "2-s2.0-85012144154", "transient": true }, "external-id-normalized-error": null, "external-id-url": null, "external-id-relationship": "self" } ] }, "work-summary": [ { "put-code": 43502281, "created-date": { "value": 1523449035679 }, "last-modified-date": { "value": 1653595164746 }, "source": { "source-orcid": null, "source-client-id": { "uri": "https://orcid.org/client/0000-0002-5982-8983", "path": "0000-0002-5982-8983", "host": "orcid.org" }, "source-name": { "value": "Scopus - Elsevier" }, "assertion-origin-orcid": { "uri": "https://orcid.org/0000-0001-8713-9213", "path": "0000-0001-8713-9213", "host": "orcid.org" }, "assertion-origin-client-id": null, "assertion-origin-name": { "value": "Casey Greene" } }, "title": { "title": { "value": "Computational approaches to study microbes and microbiomes" }, "subtitle": null, "translated-title": null }, "external-ids": { "external-id": [ { "external-id-type": "eid", "external-id-value": "2-s2.0-85012144154", "external-id-normalized": { "value": "2-s2.0-85012144154", "transient": true }, "external-id-normalized-error": null, "external-id-url": null, "external-id-relationship": "self" } ] }, "url": { "value": "http://www.scopus.com/inward/record.url?eid=2-s2.0-85012144154&partnerID=MN8TOARS" }, "type": "conference-paper", "publication-date": { "year": { "value": "2016" }, "month": null, "day": null }, "journal-title": { "value": "Pacific Symposium on Biocomputing 2016, PSB 2016" }, "visibility": "public", "path": "/0000-0001-8713-9213/work/43502281", "display-index": "0" } ] }, { "last-modified-date": { "value": 1653598065493 }, "external-ids": { "external-id": [ { "external-id-type": "wosuid", "external-id-value": "WOS:000386326200051", "external-id-normalized": { "value": "wos:000386326200051", "transient": true }, "external-id-normalized-error": null, "external-id-url": null, "external-id-relationship": "self" } ] }, "work-summary": [ { "put-code": 43716358, "created-date": { "value": 1523967901110 }, "last-modified-date": { "value": 1653598065493 }, "source": { "source-orcid": null, "source-client-id": { "uri": "https://orcid.org/client/0000-0003-1377-5676", "path": "0000-0003-1377-5676", "host": "orcid.org" }, "source-name": { "value": "ResearcherID" }, "assertion-origin-orcid": { "uri": "https://orcid.org/0000-0001-8713-9213", "path": "0000-0001-8713-9213", "host": "orcid.org" }, "assertion-origin-client-id": null, "assertion-origin-name": { "value": "Casey Greene" } }, "title": { "title": { "value": "Computational approaches to study microbes and microbiomes" }, "subtitle": null, "translated-title": null }, "external-ids": { "external-id": [ { "external-id-type": "wosuid", "external-id-value": "WOS:000386326200051", "external-id-normalized": { "value": "wos:000386326200051", "transient": true }, "external-id-normalized-error": null, "external-id-url": null, "external-id-relationship": "self" } ] }, "url": { "value": "http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000386326200051&KeyUID=WOS:000386326200051" }, "type": "conference-paper", "publication-date": { "year": { "value": "2016" }, "month": null, "day": null }, "journal-title": { "value": "Pacific Symposium on Biocomputing 2016, PSB 2016" }, "visibility": "public", "path": "/0000-0001-8713-9213/work/43716358", "display-index": "0" } ] }, { "last-modified-date": { "value": 1653595164754 }, "external-ids": { "external-id": [ { "external-id-type": "eid", "external-id-value": "2-s2.0-85015595524", "external-id-normalized": { "value": "2-s2.0-85015595524", "transient": true }, "external-id-normalized-error": null, "external-id-url": null, "external-id-relationship": "self" } ] }, "work-summary": [ { "put-code": 43502282, "created-date": { "value": 1523449035690 }, "last-modified-date": { "value": 1653595164754 }, "source": { "source-orcid": null, "source-client-id": { "uri": "https://orcid.org/client/0000-0002-5982-8983", "path": "0000-0002-5982-8983", "host": "orcid.org" }, "source-name": { "value": "Scopus - Elsevier" }, "assertion-origin-orcid": { "uri": "https://orcid.org/0000-0001-8713-9213", "path": "0000-0001-8713-9213", "host": "orcid.org" }, "assertion-origin-client-id": null, "assertion-origin-name": { "value": "Casey Greene" } }, "title": { "title": { "value": "NO-BOUNDARY THINKING IN BIOINFORMATICS" }, "subtitle": null, "translated-title": null }, "external-ids": { "external-id": [ { "external-id-type": "eid", "external-id-value": "2-s2.0-85015595524", "external-id-normalized": { "value": "2-s2.0-85015595524", "transient": true }, "external-id-normalized-error": null, "external-id-url": null, "external-id-relationship": "self" } ] }, "url": { "value": "http://www.scopus.com/inward/record.url?eid=2-s2.0-85015595524&partnerID=MN8TOARS" }, "type": "journal-article", "publication-date": { "year": { "value": "2016" }, "month": null, "day": null }, "journal-title": { "value": "Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing" }, "visibility": "public", "path": "/0000-0001-8713-9213/work/43502282", "display-index": "0" } ] }, { "last-modified-date": { "value": 1653598065538 }, "external-ids": { "external-id": [ { "external-id-type": "source-work-id", "external-id-value": "0417180825983-87", "external-id-normalized": { "value": "0417180825983-87", "transient": true }, "external-id-normalized-error": null, "external-id-url": null, "external-id-relationship": "self" } ] }, "work-summary": [ { "put-code": 43716370, "created-date": { "value": 1523967915851 }, "last-modified-date": { "value": 1653598065538 }, "source": { "source-orcid": null, "source-client-id": { "uri": "https://orcid.org/client/0000-0003-1377-5676", "path": "0000-0003-1377-5676", "host": "orcid.org" }, "source-name": { "value": "ResearcherID" }, "assertion-origin-orcid": { "uri": "https://orcid.org/0000-0001-8713-9213", "path": "0000-0001-8713-9213", "host": "orcid.org" }, "assertion-origin-client-id": null, "assertion-origin-name": { "value": "Casey Greene" } }, "title": { "title": { "value": "NO-BOUNDARY THINKING IN BIOINFORMATICS" }, "subtitle": null, "translated-title": null }, "external-ids": { "external-id": [ { "external-id-type": "source-work-id", "external-id-value": "0417180825983-87", "external-id-normalized": { "value": "0417180825983-87", "transient": true }, "external-id-normalized-error": null, "external-id-url": null, "external-id-relationship": "self" } ] }, "url": { "value": "http://www.scopus.com/inward/record.url?eid=2-s2.0-85015595524&partnerID=MN8TOARS" }, "type": "journal-article", "publication-date": { "year": { "value": "2016" }, "month": null, "day": null }, "journal-title": { "value": "Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing" }, "visibility": "public", "path": "/0000-0001-8713-9213/work/43716370", "display-index": "0" } ] }, { "last-modified-date": { "value": 1653474821420 }, "external-ids": { "external-id": [ { "external-id-type": "eid", "external-id-value": "2-s2.0-84971009612", "external-id-normalized": { "value": "2-s2.0-84971009612", "transient": true }, "external-id-normalized-error": null, "external-id-url": null, "external-id-relationship": "self" } ] }, "work-summary": [ { "put-code": 28451715, "created-date": { "value": 1480423769496 }, "last-modified-date": { "value": 1653474821420 }, "source": { "source-orcid": null, "source-client-id": { "uri": "https://orcid.org/client/0000-0002-5982-8983", "path": "0000-0002-5982-8983", "host": "orcid.org" }, "source-name": { "value": "Scopus - Elsevier" }, "assertion-origin-orcid": { "uri": "https://orcid.org/0000-0001-8713-9213", "path": "0000-0001-8713-9213", "host": "orcid.org" }, "assertion-origin-client-id": null, "assertion-origin-name": { "value": "Casey Greene" } }, "title": { "title": { "value": "Nothing but a hound dog" }, "subtitle": null, "translated-title": null }, "external-ids": { "external-id": [ { "external-id-type": "eid", "external-id-value": "2-s2.0-84971009612", "external-id-normalized": { "value": "2-s2.0-84971009612", "transient": true }, "external-id-normalized-error": null, "external-id-url": null, "external-id-relationship": "self" } ] }, "url": { "value": "http://www.scopus.com/inward/record.url?eid=2-s2.0-84971009612&partnerID=MN8TOARS" }, "type": "journal-article", "publication-date": { "year": { "value": "2016" }, "month": null, "day": null }, "journal-title": { "value": "Science Translational Medicine" }, "visibility": "public", "path": "/0000-0001-8713-9213/work/28451715", "display-index": "0" } ] }, { "last-modified-date": { "value": 1653598065549 }, "external-ids": { "external-id": [ { "external-id-type": "source-work-id", "external-id-value": "0417180825983-88", "external-id-normalized": { "value": "0417180825983-88", "transient": true }, "external-id-normalized-error": null, "external-id-url": null, "external-id-relationship": "self" } ] }, "work-summary": [ { "put-code": 43716372, "created-date": { "value": 1523967915860 }, "last-modified-date": { "value": 1653598065549 }, "source": { "source-orcid": null, "source-client-id": { "uri": "https://orcid.org/client/0000-0003-1377-5676", "path": "0000-0003-1377-5676", "host": "orcid.org" }, "source-name": { "value": "ResearcherID" }, "assertion-origin-orcid": { "uri": "https://orcid.org/0000-0001-8713-9213", "path": "0000-0001-8713-9213", "host": "orcid.org" }, "assertion-origin-client-id": null, "assertion-origin-name": { "value": "Casey Greene" } }, "title": { "title": { "value": "Nothing but a hound dog" }, "subtitle": null, "translated-title": null }, "external-ids": { "external-id": [ { "external-id-type": "source-work-id", "external-id-value": "0417180825983-88", "external-id-normalized": { "value": "0417180825983-88", "transient": true }, "external-id-normalized-error": null, "external-id-url": null, "external-id-relationship": "self" } ] }, "url": { "value": "http://www.scopus.com/inward/record.url?eid=2-s2.0-84971009612&partnerID=MN8TOARS" }, "type": "journal-article", "publication-date": { "year": { "value": "2016" }, "month": null, "day": null }, "journal-title": { "value": "Science Translational Medicine" }, "visibility": "public", "path": "/0000-0001-8713-9213/work/43716372", "display-index": "0" } ] }, { "last-modified-date": { "value": 1653474821414 }, "external-ids": { "external-id": [ { "external-id-type": "eid", "external-id-value": "2-s2.0-84971231452", "external-id-normalized": { "value": "2-s2.0-84971231452", "transient": true }, "external-id-normalized-error": null, "external-id-url": null, "external-id-relationship": "self" } ] }, "work-summary": [ { "put-code": 28451714, "created-date": { "value": 1480423769495 }, "last-modified-date": { "value": 1653474821414 }, "source": { "source-orcid": null, "source-client-id": { "uri": "https://orcid.org/client/0000-0002-5982-8983", "path": "0000-0002-5982-8983", "host": "orcid.org" }, "source-name": { "value": "Scopus - Elsevier" }, "assertion-origin-orcid": { "uri": "https://orcid.org/0000-0001-8713-9213", "path": "0000-0001-8713-9213", "host": "orcid.org" }, "assertion-origin-client-id": null, "assertion-origin-name": { "value": "Casey Greene" } }, "title": { "title": { "value": "Unsupervised feature construction and knowledge extraction from genome-wide assays of breast cancer with denoising autoencoders" }, "subtitle": null, "translated-title": null }, "external-ids": { "external-id": [ { "external-id-type": "eid", "external-id-value": "2-s2.0-84971231452", "external-id-normalized": { "value": "2-s2.0-84971231452", "transient": true }, "external-id-normalized-error": null, "external-id-url": null, "external-id-relationship": "self" } ] }, "url": { "value": "http://www.scopus.com/inward/record.url?eid=2-s2.0-84971231452&partnerID=MN8TOARS" }, "type": "conference-paper", "publication-date": { "year": { "value": "2015" }, "month": null, "day": null }, "journal-title": { "value": "20th Pacific Symposium on Biocomputing, PSB 2015" }, "visibility": "public", "path": "/0000-0001-8713-9213/work/28451714", "display-index": "0" } ] }, { "last-modified-date": { "value": 1653598065682 }, "external-ids": { "external-id": [ { "external-id-type": "source-work-id", "external-id-value": "0417180825986-103", "external-id-normalized": { "value": "0417180825986-103", "transient": true }, "external-id-normalized-error": null, "external-id-url": null, "external-id-relationship": "self" } ] }, "work-summary": [ { "put-code": 43716388, "created-date": { "value": 1523967915952 }, "last-modified-date": { "value": 1653598065682 }, "source": { "source-orcid": null, "source-client-id": { "uri": "https://orcid.org/client/0000-0003-1377-5676", "path": "0000-0003-1377-5676", "host": "orcid.org" }, "source-name": { "value": "ResearcherID" }, "assertion-origin-orcid": { "uri": "https://orcid.org/0000-0001-8713-9213", "path": "0000-0001-8713-9213", "host": "orcid.org" }, "assertion-origin-client-id": null, "assertion-origin-name": { "value": "Casey Greene" } }, "title": { "title": { "value": "Unsupervised feature construction and knowledge extraction from genome-wide assays of breast cancer with denoising autoencoders" }, "subtitle": null, "translated-title": null }, "external-ids": { "external-id": [ { "external-id-type": "source-work-id", "external-id-value": "0417180825986-103", "external-id-normalized": { "value": "0417180825986-103", "transient": true }, "external-id-normalized-error": null, "external-id-url": null, "external-id-relationship": "self" } ] }, "url": { "value": "http://www.scopus.com/inward/record.url?eid=2-s2.0-84971231452&partnerID=MN8TOARS" }, "type": "conference-paper", "publication-date": { "year": { "value": "2015" }, "month": null, "day": null }, "journal-title": { "value": "20th Pacific Symposium on Biocomputing, PSB 2015" }, "visibility": "public", "path": "/0000-0001-8713-9213/work/43716388", "display-index": "0" } ] }, { "last-modified-date": { "value": 1653405603906 }, "external-ids": { "external-id": [ { "external-id-type": "wosuid", "external-id-value": "MEDLINE:25592575", "external-id-normalized": { "value": "medline:25592575", "transient": true }, "external-id-normalized-error": null, "external-id-url": null, "external-id-relationship": "self" } ] }, "work-summary": [ { "put-code": 18634055, "created-date": { "value": 1442927544631 }, "last-modified-date": { "value": 1653405603906 }, "source": { "source-orcid": null, "source-client-id": { "uri": "https://orcid.org/client/0000-0003-1377-5676", "path": "0000-0003-1377-5676", "host": "orcid.org" }, "source-name": { "value": "ResearcherID" }, "assertion-origin-orcid": { "uri": "https://orcid.org/0000-0001-8713-9213", "path": "0000-0001-8713-9213", "host": "orcid.org" }, "assertion-origin-client-id": null, "assertion-origin-name": { "value": "Casey Greene" } }, "title": { "title": { "value": "Unsupervised feature construction and knowledge extraction from genome-wide assays of breast cancer with denoising autoencoders." }, "subtitle": null, "translated-title": null }, "external-ids": { "external-id": [ { "external-id-type": "wosuid", "external-id-value": "MEDLINE:25592575", "external-id-normalized": { "value": "medline:25592575", "transient": true }, "external-id-normalized-error": null, "external-id-url": null, "external-id-relationship": "self" } ] }, "url": { "value": "http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=MEDLINE&KeyUT=MEDLINE:25592575&KeyUID=MEDLINE:25592575" }, "type": "journal-article", "publication-date": { "year": { "value": "2015" }, "month": null, "day": null }, "journal-title": { "value": "Pacific Symposium on Biocomputing. 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"assertion-origin-name": { "value": "Casey Greene" } }, "title": { "title": { "value": "Applications of bioinformatics to non-coding RNAs in the era of next-generation sequencing" }, "subtitle": null, "translated-title": null }, "external-ids": { "external-id": [ { "external-id-type": "eid", "external-id-value": "2-s2.0-84905885881", "external-id-normalized": { "value": "2-s2.0-84905885881", "transient": true }, "external-id-normalized-error": null, "external-id-url": null, "external-id-relationship": "self" } ] }, "url": { "value": "http://www.scopus.com/inward/record.url?eid=2-s2.0-84905885881&partnerID=MN8TOARS" }, "type": "conference-paper", "publication-date": { "year": { "value": "2014" }, "month": null, "day": null }, "journal-title": { "value": "19th Pacific Symposium on Biocomputing, PSB 2014" }, "visibility": "public", "path": "/0000-0001-8713-9213/work/19471904", "display-index": "0" } ] }, { "last-modified-date": { "value": 1653598065688 }, "external-ids": { "external-id": 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"value": "ResearcherID" }, "assertion-origin-orcid": { "uri": "https://orcid.org/0000-0001-8713-9213", "path": "0000-0001-8713-9213", "host": "orcid.org" }, "assertion-origin-client-id": null, "assertion-origin-name": { "value": "Casey Greene" } }, "title": { "title": { "value": "An expert knowledge-guided mutation operator for genome-wide genetic analysis using genetic programming" }, "subtitle": null, "translated-title": null }, "external-ids": { "external-id": [ { "external-id-type": "source-work-id", "external-id-value": "0417180825475-141", "external-id-normalized": { "value": "0417180825475-141", "transient": true }, "external-id-normalized-error": null, "external-id-url": null, "external-id-relationship": "self" } ] }, "url": { "value": "http://www.scopus.com/inward/record.url?eid=2-s2.0-38349045395&partnerID=MN8TOARS" }, "type": "book", "publication-date": { "year": { "value": "2007" }, "month": null, "day": null }, "journal-title": { "value": "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)" }, "visibility": "public", "path": "/0000-0001-8713-9213/work/43716411", "display-index": "0" } ] } ] ```

It seems like possibly a big lift to make a mapping between all of these ORCID id types, and there might be no mapping for some of them. Maybe we could somehow determine what the most common non-doi types are and support those. And if Casey's ORCID is any indication, eid and wosuid seem to be it... 🤷‍♀️

dhimmel commented 1 year ago

Scopus

Okay so eid refers to Scopus. For example, eid:2-s2.0-85012144154 refers to the study "Computational approaches to study microbes and microbiomes" with a URL of http://www.scopus.com/inward/record.url?eid=2-s2.0-85012144154&partnerID=MN8TOARS. Based on this blog post, we can also reformat the URL to be https://www.scopus.com/record/display.uri?eid=2-s2.0-85012144154&origin=resultslist. Both of these resolve in my browser, but I can't get them to work programtically with curl or manubot cite. See also Wikidata P1154. Too bad the ORCID data doesn't include other more accessible identifiers like pmc:PMC4832978, pubmed:26776218, or doi:10.1142/9789814749411_0051 (despite the scopus record contained some of these identifiers).

Possible solutions:

Web of Science

Looks like you can get a URL for the Web of Science records like https://www.webofscience.com/wos/woscc/full-record/WOS:000411479100034 (see Wikidata P8372. This does work programatically, but WoS doesn't set complete citation metadata in the HTML and/or Zotero translator needs tweaks.

Possible solutions:

if Casey's ORCID is any indication, eid and wosuid seem to be it

Casey has probably done Scopus to ORCID and this.