Enable citation directly from bioconductor
Hi,
Bioconductor website holds 1700+ software packages with high citations.
However, zotero could not grab author and other information correctly from the bioconductor software package webpages. For example,
https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html
So I want to make a feature request for Zotero to extract info from bioconductor package webpages directly. I would appreciate for any responses.
Best,
Qiang
Bioconductor website holds 1700+ software packages with high citations.
However, zotero could not grab author and other information correctly from the bioconductor software package webpages. For example,
https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html
So I want to make a feature request for Zotero to extract info from bioconductor package webpages directly. I would appreciate for any responses.
Best,
Qiang
(R packages can provide citation metadata within the R environment, see https://bioconductor.org/help/faq/#citation-faq and https://stat.ethz.ch/R-manual/R-devel/library/utils/html/citation.html; e.g.: )
Also, on the bioconductor pages, right-click --> Save to Zotero (DOI) will at least get you the basic info (for packages with DOI).
Not sure if we want to build a separate scrape here that needs to be maintained.
Thanks for looking into this issue. I'll report this to Bioconductor core team (where I am a member), and see if there is anything we can do about the DOI and related data. Hope this is just an issue that could be fixed on our end. Will follow back later.
~ Qian
$ curl -LH "Accept: application/vnd.datacite.datacite+xml" https://doi.org/10.18129/B9.bioc.SummarizedExperiment
.Every author should have their own
creator
tag. The other info noted by hubuntu as missing is also not in there.<?xml version="1.0" encoding="UTF-8"?>
<resource xmlns="http://datacite.org/schema/kernel-4" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4/metadata.xsd">
<identifier identifierType="DOI">10.18129/B9.BIOC.SUMMARIZEDEXPERIMENT</identifier>
<creators>
<creator>
<creatorName>Martin Morgan, Valerie Obenchain, Jim Hester, Hervé Pagès</creatorName>
</creator>
</creators>
<titles>
<title>SummarizedExperiment</title>
</titles>
<publisher>Bioconductor</publisher>
<publicationYear>2017</publicationYear>
<resourceType resourceTypeGeneral="Software"/>
</resource>
Thanks for the info, and the code above helps! We did find the Bioconductor website metadata and DOI containing non-complete info. We are working to update those so that Zotero could add Bioc package webpages directly.
Best,
Qian
I am helping to test the standardized metadata for Bioconductor using Dublin Core.
I set the DC.type to "Software", but zotero could not recognize it to "Computer program". The Item Type is still "Web Page". Some of the DC type works, such as article, film...
Any suggestion to make zotero work with "software" in metadata? Thanks!
Here is the test page.
http://awesome-davinci-6f193c.netlify.com/
<html>
<head>
<title>SummarizedExperiment: SummarizedExperiment container</title>
<meta name="DC.creator" content="Morgan, Martin"/>
<meta name="DC.creator" content="Obenchain, Valerie"/>
<meta name="DC.creator" content="Hester, Jim"/>
<meta name="DC.creator" content="Pagès, Hervé"/>
<meta name="DCTERMS.dateAccepted" content="2015-01-01T23:18:49Z" scheme="DCTERMS.W3CDTF"/>
<meta name="DCTERMS.available" content="2015-01-01T23:18:49Z" scheme="DCTERMS.W3CDTF"/>
<meta name="DC.identifier" content="10.18129/B9.bioc.SummarizedExperiment"/>
<meta name="DC.identifier" content="https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html" scheme="DCTERMS.URI"/>
<meta name="DC.description" content="The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples."/>
<meta name="DC.title" content="SummarizedExperiment:SummarizedExperiment container"/>
<meta name="DC.type" content="Software"/>
<meta name="DC.version" content="0.1">
</head>
<title>Bioconductor - SummarizedExperiment</title>
<body>
[1]M. Morgan, V. Obenchain, J. Hester, and H. Pagès, “SummarizedExperiment:SummarizedExperiment container.” [Online]. Available: http://127.0.0.1:8081/test.html. [Accessed: 15-Jul-2019].
</body>
</html>
I have decided to write a translator instead. The documents are great. I made one and it works well in my manual test, but failed in the pull check step. I am new to javascript... Any help would be appreciated. Thanks!
https://github.com/zotero/translators/pull/1983