{ "version": "https://jsonfeed.org/version/1.1", "title": "chem-bla-ics", "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.", "home_page_url": "https://chem-bla-ics.linkedchemistry.info/", "feed_url": "https://chem-bla-ics.linkedchemistry.info/2007/07/31/rdf-ing-molecular-space.json", "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png", "language": "en", "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286", "_orcid": "0000-0001-7542-0286" } ], "items": [ { "id": "https://doi.org/10.59350/9r29x-8y455", "url": "https://chem-bla-ics.linkedchemistry.info/2007/07/31/rdf-ing-molecular-space.html", "title": "RDF-ing molecular space", "content_html": "

RDF might be the solution we are looking for to get a grip\non the huge amount of information we are facing. microformats ,\nand RDFa , are just solutions along the way,\nand Gleaning Resource Descriptions from Dialects of Languages (GRDDL) might be\nan important tool to get the web RDF-ied.

\n\n

One important aspect of RDF is that any resource has a unique URI.\nThese make look like a URL or even like urn:doi:10.1186/1471-2105-8-59. The recent blogs by Pierre\n(URL +1, LSID -1) and Roderic\n(Rethinking LSIDs versus HTTP URI)\nillustrate the pro and cons of the different alternatives.

\n\n

bioGUID

\n\n

As usual, the bioinformaticians are less conservative and ahead of chemists in trying new options, and several interesting\nwebsite have emerged. For example, bioGUID makes the bridge between a simple URI and a resolvable URL.\nAnd, importantly, it spit RDF. This is the output for http://bioguid.info/doi:10.1109/MIS.2006.62:

\n\n
<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<?xml-stylesheet type=\"text/xsl\" href=\"http://bioguid.info/xsl/html.xsl\"?>\n<rdf:RDF xmlns:bioguid=\"http://bioguid.info/schema/0.1/\" \n  xmlns:rdfs=\"http://www.w3.org/2000/01/rdf-schema#\"\n  xmlns:rss=\"http://purl.org/rss/1.0/\" \n  xmlns:prism=\"http://prismstandard.org/namespaces/1.2/basic/\"\n  xmlns:dcterms=\"http://purl.org/dc/terms/\" \n  xmlns:dc=\"http://purl.org/dc/elements/1.1/\"\n  xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\">\n  <rdf:Description rdf:about=\"http://bioguid.info/doi:10.1109/MIS.2006.62\">\n    <rdf:type rdf:resource=\"http://bioguid.info/schema/0.1/Publication\"/>\n    <rdfs:comment>Generated by transforming XML returned by CrossRef's\n      OpenURL service.</rdfs:comment>\n    <dc:creator>Shadbolt</dc:creator>\n    <dc:title>The Semantic Web Revisited</dc:title>\n    <dcterms:issued>2006</dcterms:issued>\n\n    <prism:publicationDate>2006</prism:publicationDate>\n    <dc:identifier rdf:resource=\"doi:10.1109/MIS.2006.62\"/>\n    <rdfs:comment>info URI scheme</rdfs:comment>\n    <dc:identifier rdf:resource=\"info:doi/10.1109/MIS.2006.62\"/>\n    <rdfs:comment>CrossRef resolver</rdfs:comment>\n    <rss:link>http://dx.doi.org/10.1109/MIS.2006.62</rss:link>\n    <prism:publicationName>IEEE Intelligent Systems</prism:publicationName>\n\n    <prism:volume>21</prism:volume>\n    <prism:number>3</prism:number>\n    <prism:startingPage>96</prism:startingPage>\n    <prism:issn>10947167</prism:issn>\n  </rdf:Description>\n</rdf:RDF>\n
\n\n

(BTW, interesting is the use of XSLT to create HTML; it’s doing the opposite of GRDDL! And this is probably the right way. Cheers Roderic!)

\n\n

InChI

\n\n

I wanted something similar for molecules. The unique identifier is the InChI, of course. The InChI itself is\nnot a proper URI, so I set up a webpage to work around that (if only I had realized this some time ago, I would have urged IUPAC to use\nthe prefix ‘inchi:’ instead of ‘InChI=’). The result is, currently, looking like\nhttp://cb.openmolecules.net/rdf/rdf.php?InChI=1/CH4/h1H4.\nI do not use a XSLT yet, but will do so shortly. The RDF looks like:

\n\n
<rdf:RDF\nxmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\"\nxmlns:iupac=\"http://www.iupac.org/\">\n\n<rdf:Description\n rdf:about=\"http://cb.openmolecules.net/rdf/?InChI=1/CH4/h1H4\">\n\n <iupac:inchi>InChI=1/CH4/h1H4</iupac:inchi>\n\n <pubchem:cid xmlns:pubchem=\"http://pubchem.ncbi.nlm.nih.gov/#\">297</pubchem:cid>\n <pubchem:name xmlns:pubchem=\"http://pubchem.ncbi.nlm.nih.gov/#\">methane</pubchem:name>\n <cb:discussedBy xmlns:cb=\"http://cb.openmolecules.net/#\">http://chemistrylabnotebook.blogspot.com/2007/04/space-final-frontier.html</cb:discussedBy>\n <cb:discussedBy xmlns:cb=\"http://cb.openmolecules.net/#\">http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=299</cb:discussedBy>\n <cb:discussedBy xmlns:cb=\"http://cb.openmolecules.net/#\">http://chem-bla-ics.blogspot.com/2006/12/smiles-cas-and-inchi-in-blogs.html</cb:discussedBy>\n <cb:discussedBy xmlns:cb=\"http://cb.openmolecules.net/#\">http://chem-bla-ics.blogspot.com/2007/02/invisible-inchis.html</cb:discussedBy>\n\n</rdf:Description>\n\n</rdf:RDF>\n
\n\n

The system uses PHP to create the output, and has a basis pluggable system: a plugin basically spits a RDF fragment for\nthe given InChI, and at this moment it only has a plugin for Cb, but I plan a few more.\nIt needs some tuning and any and all feedback is most welcome. Note that the actual URI might change a bit.

", "summary": "RDF might be the solution we are looking for to get a grip on the huge amount of information we are facing. microformats , and RDFa , are just solutions along the way, and Gleaning Resource Descriptions from Dialects of Languages (GRDDL) might be an important tool to get the web RDF-ied.", "date_published": "2007-07-31T00:00:00+00:00", "date_modified": "2025-07-30T00:00:00+00:00", "tags": ["chemistry","rdf","inchi","rdfa"], "_citations": [ { "url": "https://doi.org/10.1016/j.drudis.2008.03.015", "doi": "10.1016/j.drudis.2008.03.015" , "cito": [ "citesForInformation" ] } ], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }