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NeuroCommons RDF Library - sources and terms

This page lists the contents of the NeuroCommons RDF library with the terms of use of each item. The below provides information that to the best of our knowledge reflects the terms under which Science Commons and others may use these resources. This is not legal advice and does not constitute a license.

The conversions to RDF of some (not all) of the sources listed here were performed as part of the activity of the W3C Semantic Web Health Care and Life Sciences (HCLS) Interest Group, in which Science Commons participated.

RDF bundle name Last modifiedSize Description RDF conversion by Terms
aba-2007-08-07.tgz 22-Sep-2007   51M SC's extract of Allen Brain Atlas metadata from their web site. Web site was read on 26 Feb 2007 or shortly before Alan Ruttenberg, SC terms of use
addgene.ttl 16-May-2007 1.1M Addgene catalog (tab-delimited file) Jonathan Rees, SC provided to Science Commons by Addgene
bams-from-swanson-98-4-23-07.owl 23-Apr-2007 5.6M BAMS John Barkley, NIST released without contract
galen.tgz 22-Sep-2007 1.9M Galen from co-ode.org - released without contract
gene-owl.tgz 08-May-2007 7.7M Extract from ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz Alan Ruttenberg, SC NCBI Copyright and Disclaimers
gene-pubmed.ttl.tgz 08-May-2007 1.5M Extract from Entrez Gene Ray Hookway, HP / Jonathan Rees, SC NCBI Copyright and Disclaimers
goa-in-owl.tgz 16-May-2007 73M GO annotations from NCBI and EBI Alan Ruttenberg, SC NCBI Copyright and Disclaimers; EBI terms of use
homologene.tgz 16-May-2007 626K Homologene Alan Ruttenberg, SC NCBI Copyright and Disclaimers
medline-mesh.tgz 16-May-2007 758M List of all associations of MeSH headings to papers indexed by Medline extracted from 2007 Medline baseline distribution Jonathan Rees, SC License Agreement to Lease NLM Databases in Machine-Readable Form - see below
medline-titles.tgz 16-May-2007 670M Extracted from 2007 Medline baseline distribution Jonathan Rees, SC see below
mesh-qualified-headings.ttl.gz 30-Apr-2007 13M NLM 2007 MeSH descriptor/qualifier pairs Jonathan Rees, SC MeSH MOU
mesh-skos.tgz 16-May-2007 13M NLM 2007 MeSH van Assem et al MeSH MOU
mesh07-eswc06.rdfs 28-Jun-2007 2.2K van Assem et al's ontology (used by output of MeSH to SKOS conversion) - released without contract
neurocommons-text-mining.tgz 05-May-2007 24M NeuroCommons text mining pilot - extracted from Temis software applied to 7% of Medline records (SC) - released without contract
obo-all.tgz 22-Sep-2007 36M All OBO ontologies, from berkeleybop - released without contract
obo-in-owl.tgz 16-May-2007 2.6M selected OBO ontologies, downloaded ~21 April 2007, augmented with inferred relations Alan Ruttenberg, SC released without contract
sciencecommons.owl 28-Jun-2007 19K ad hoc ontology from Science Commons used by the output of of several of the conversion scripts - released without contract
senselab.tgz 16-May-2007 216K From Yale Senselab Cheung, Samwald, et al., Yale released without contract
SKOS SKOS - W3C software licensing rules
Reactome records 23-May-2008 21M Reactome records, on the way to BioPAX-OBO. See discussion. N-Triples format. Alan Ruttenberg, SC / Andrea Splendiani, Univ. Milano-Bicocca Reactome Disclaimer

All conversion scripts from Science Commons are available under a BSD license.

See also our FAQ on databases and Creative Commons.

About the MeSH extraction

The Medical Subject Heading (MeSH) information was created and provided, and is maintained, by the U.S. National Library of Medicine. The information provided here, which is a conversion to RDF by van Assem's script (ESWC 2006), is from the 2007 version of MeSH.

About the Medline extraction

NLM has asked Science Commons to issue the following notice regarding downloading and subsequent re-use of portions of NLM databases obtained from its products:

"Unless otherwise prohibited, organizations or institutions may download small amounts of NLM-produced citations for redistribution. For MEDLINE, this is about 1,000 per month or 12,000 records for each year of coverage. For other MEDLARS databases, it is approximately 25% of the records in the file except for AIDSLINEŽ, AIDSTRIALS, and AIDSDRUGS which may be downloaded in their entirety. Since NLM makes corrections and enhancements to and performs maintenance on these records at least annually, you should plan to replace or correct the records once a year to ensure that they are still correct and searchable as a group."

"NLM databases are produced by a U.S. government agency and as such the contents are not covered by copyright domestically. They may be copyrighted outside the U.S. Some NLM produced data is from copyrighted publications of the respective copyright claimants. Users of the NLM databases are solely responsible for compliance with any copyright restrictions and are referred to the publication data appearing in the bibliographic citations, as well as to the copyright notices appearing in the original publications, all of which are incorporated by reference. Users should consult legal counsel before using NLM-produced records to be certain that their plans are in compliance with appropriate laws."

"All records must be identified as being derived from NLM databases."

"Some material in the NLM databases is from copyrighted publications of the respective copyright claimants. Users of the NLM databases are solely responsible for compliance with any copyright restrictions and are referred to the publication data appearing in the bibliographic citations, as well as to the copyright notices appearing in the original publications, all of which are hereby incorporated by reference."

Please observe that the RDF for Medline provided by Science Commons does not include the text of any article abstract. The only fields extracted at this time are the subject headings (MeSH) and minimal reference information.

Jonathan Rees
jar@creativecommons.org
20 December 2007, updated 25 July 2008


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