Added additional resources

licenses/README.md

@@ -5,4 +5,16 @@ License table:
 | -------- | ------- | ------ |
 | Disease Ontology | [CC-BY 3.0](https://creativecommons.org/licenses/by/3.0/) | [2015-08-20](http:https://disease-ontology.org/resources/) |
 | DrugBank 4.2 | [custom](custom/DrugBank.md) | [2015-08-20](http:https://www.drugbank.ca/) |
+| Entrez Gene | | |
 | Uberon | | |
+| MeSH | [custom](custom/MeSH.md) | [2015-08-21](https://www.nlm.nih.gov/mesh/termscon.html) |
+| WikiPathways | [CC-BY 3.0](https://creativecommons.org/licenses/by/3.0/) / [custom](custom/WikiPathways.md) | [2015-08-20](http:https://www.wikipathways.org/index.php/WikiPathways:License_Terms) |
+| WikiPathways | [CC-BY 3.0](https://creativecommons.org/licenses/by/3.0/) / [custom](custom/WikiPathways.md) | [2015-08-20](http:https://www.wikipathways.org/index.php/WikiPathways:License_Terms) |
+| MSigDB | [custom](custom/MSigDB.txt) | [2015-08-20](http:https://www.broadinstitute.org/gsea/msigdb/download_file.jsp?filePath=/resources/licenses/gsea_msigdb_license.txt) |
+| MSigDB | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/legalcode) | [2015-08-21](http:https://geneontology.org/page/use-and-license) |
+| GWAS Catalog | | |
+| DOAF | | |
+| ADEPTUS | | |
+| MEDLINE | [custom](custom/MEDLINE.md) | [2015-08-21](http:https://www.nlm.nih.gov/databases/journal.html) |
+| Bgee | | |
+| BindingDB | [custom (CC-BY 3.0 & CC-BY-SA 3.0)](custom/BingindDB.md) | [2015-08-21](https://www.bindingdb.org/bind/info.jsp) |

licenses/custom/BindingDB.md

@@ -0,0 +1,34 @@
+Retrieved from https://www.bindingdb.org/bind/info.jsp on 2015-08-21.
+
+# Info
+
+**Info**
+
+* * *
+
+BindingDB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of proteins considered to be candidate drug-targets with ligands that are small, drug-like molecules. BindingDB supports medicinal chemistry and drug discovery via literature awareness and development of structure-activity relations (SAR and QSAR); validation of computational chemistry and molecular modeling approaches such as docking, scoring and free energy methods; chemical biology and chemical genomics; and basic studies of the physical chemistry of molecular recognition. BindingDB also includes a small collection of host-guest binding data of interest to chemists studying supramolecular systems.
+
+The data collection derives from a variety of measurement techniques, including enzyme inhibition and kinetics, isothermal titration calorimetry, NMR, and radioligand and competition assays. BindingDB includes data extracted from the literature and patents by the BindingDB project, selected PubChem confirmatory BioAssays, and ChEMBL entries for which a well defined protein target ("TARGET_TYPE='PROTEIN'") is provided. Data extracted by BindingDB typically includes more details regarding experimental conditions, etc. BindingDB currently contains about 1,142,124 binding data for 7,032 proteins and over 495,498 drug-like molecules. Data imported from ChEMBL are provided under their [Creative Commons Attribution-Share Alike 3.0 Unported License][1]. All data curated by BindingDB staff are provided under the [Creative Commons Attribution 3.0 License][2].
+
+**BindingDB Affinity Statistics**
+
+![][3]
+
+**References**
+
+1. Liu,T., Lin,Y., Wen,X., Jorrisen, R.N. and Gilson,M.K. _BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities_ Nucleic Acids Research _35:D198-D201_ (2007).[[pdf]][4]
+2. Chen,X., Lin,Y. and Gilson,M.K. _The Binding Database: Overview and User's Guide_ Biopolymers Nucleic Acid Sci. _61:127-141_ (2002).[[pdf]][5]
+3. Chen,X., Lin,Y., Liu,M. and Gilson,M.K. _The Binding Database: Data Management and Interface Design_ Bioinformatics _18:130-139_(2002).[[pdf]][6]
+4. Chen,X., Liu,M., and Gilson,M.K. _Binding DB: A web-accessible molecular recognition database_ J. Combi. Chem. High-Throughput Screen _4:719-725_(2001).[[pdf]][7]
+
+
+
+
+
+[1]: https://www.ebi.ac.uk/chembl/about
+[2]: https://creativecommons.org/licenses/by/3.0/us/
+[3]: https://www.bindingdb.org/img/PlotBDBhist.gif
+[4]: /bind/bindingdb-nar-2007.pdf
+[5]: /bind/bindingdb-bnas-2002.pdf
+[6]: /bind/bindingdb-bif-2002.pdf
+[7]: /bind/bindingdb-jcchts-2001.pdf

licenses/custom/MEDLINE.md

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+Retrieved from https://www.nlm.nih.gov/databases/journal.html on 2015-08-21.
+
+***
+
+# Leasing Journal Citations (MEDLINE®/PubMed® including OLDMEDLINE)
+
+**Data Content**
+[MEDLINE][1], the primary component of [PubMed®][2], is the NLM's premier citation database. MEDLINE's subject scope is biomedicine and health, broadly defined to encompass those areas of the life sciences, behavioral sciences, chemical sciences, and bioengineering.
+
+MEDLINE citation data comprises approximately 91% of the data distributed to MEDLINE/PubMed licensees. The other categories of records that reside in PubMed and are distributed to licensees are:
+
+1. the out-of-scope citations from a few selectively indexed MEDLINE journals (primarily covering general science and general chemistry) for which the life sciences articles are indexed for MEDLINE;
+2. in-process citations which provide a record for an article before it is indexed with MeSH and added to MEDLINE or converted to out-of-scope status;
+3. some citations in the [OLDMEDLINE][3] subset that have not yet been updated with current vocabulary and converted to MEDLINE status;
+4. some citations in PubMed that precede the date a journal was selected for MEDLINE indexing if the citations are submitted after late 2003 to NLM electronically by the publishers;
+5. starting in summer 2005, prospective citations to articles from non-MEDLINE journals that submit full text to PubMed Central and are thus cited in PubMed.
+
+NLM now exports over 98% of PubMed records to MEDLINE/PubMed licensees. The approximately 2% of the records not exported to MEDLINE/PubMed licensees are those tagged [PubMed - as supplied by publisher] in PubMed. These are mostly records recently added directly to PubMed via electronic submission from a publisher, most of which are soon to proceed to the next stage, at which time the record will be exported. Most other non-exported records are either: older citations for the relatively few non-MEDLINE journals in PubMed; citations to MEDLINE journals prior to their date of selection for MEDLINE which were submitted electronically by the publishers before late July 2003; or citations electronically submitted for articles that appear on the Web in advance of the journal issue's release (i.e., ahead of print citations). Following publication of the completed issue, the item will be queued for issue level review and released in In-Data-Review status. All "publisher-supplied" citations have not been reviewed for accurate bibliographic data. Also see the Fact Sheet ["MEDLINE, PubMed, and PMC (PubMed Central): How are they different?"][4].
+
+The group of elements that reside in PubMed records are not distributed to NLM licensees.
+
+NLM does not provide search software.
+
+**Specifications and Access**
+NLM distributes MEDLINE/PubMed in [XML][5] format via ftp. See [MEDLINE Characters][6] for information on use of diacritical marks and UTF-8 encoding. Links to the [DTDs][7] and other information/documentation, including [MEDLINE/PubMed XML data element descriptions][8], are available. Also see [MEDLINE/PubMed Data][9].
+
+A completely [maintained][10] MEDLINE/PubMed baseline database now containing over 25 million records is available each December.
+
+Each year's baseline database is a complete reload for continuing licensees. The current (2015) baseline database requires 113.9 GB disk space uncompressed; 15.8 GB compressed. Subsequent update files distributed after the baseline files contain new, revised, and deleted records. They are generally available seven days each week and should be applied by licensees regularly.
+
+In addition to, or instead of, mounting the XML data locally, licensees have access to the MEDLINE/PubMed Baseline Repository (MBR) Query Tool which is available from a link on the [MBR main page][11]. The MBR home page contains links to various freely accessible resources; however the Query Tool is restricted to NLM's registered MEDLINE/PubMed licensees. The MBR Query Tool provides Web access to the baseline databases 2002 and forward. It permits searching by MeSH Headings, Subheadings, MeSH Heading/Subheading combinations, Names of Substances (MeSH Supplementary Concept Records), and PMID. Users can limit or filter by Date Created, Date Completed, Date Last Revised, Publication Year, and Status. Citations retrieved are available in both XML Format and PubMed's MEDLINE ASCII Display Format.
+
+**Sample NLM Data**
+[Sample MEDLINE/PubMed data][12] are available. A license agreement is not needed for sample data.
+
+**How to Lease
+**NLM leases MEDLINE/PubMed to U.S. and non-US individuals or organizations.
+
+To request a license, complete and submit the License Request Form after reading and accepting the electronic [License Agreement for NLM Data][13].
+
+The end of the each MEDLINE production year is mid-November and the new year's baseline files will be available for complete reload approximately one month later. Depending on the time of year, prospective licensees may wish to consider waiting until December to first get the data to avoid a reload of the new year's files shortly after initial receipt of the data. See Additional Information below.
+
+**Alternatives to Leasing**
+MEDLINE/PubMed may be [downloaded][14] for personal use and a single copy of downloaded data may be redistributed. Small amounts of MEDLINE/PubMed data may be [retrieved from PubMed][15] for redistribution without entering into a formal licensing agreement. See [Information on Copyright][14] for additional details.
+
+**Additional Information**
+MEDLINE/PubMed update files contain new and revised versions of records, and deleted records. Update files are generally available to licensees at noon EST Tuesday-Saturday. During several weeks each November and December only records in in-data-review and in-process status are distributed as NLM prepares for and performs annual data maintenance. Various types of maintenance actions, sometimes affecting large numbers of records, also take place during the year. Thus, licensees should process the revised records as well as new and deleted records in the update files regularly.
+
+Announcements and documentation for licensees are posted at the [Information for Licensees of NLM Data][16] page. Licensees are also encouraged to read the [_NLM Technical Bulletin_][17] and to subscribe to NLM's e-mail alert, [NLM-Announces][18].
+
+The [MeSH Vocabulary][19], a companion database for MEDLINE, may be downloaded at no cost after completion of a brief Memorandum of Understanding.
+
+The [IndexCatalogue][20] data may be downloaded at not cost (no license required).
+
+Information about journals cited in MEDLINE/PubMed is found in:
+
+1. [_The List of Serials Indexed for Online Users_][21] (download in XML format; does not cover the OLDMEDLINE subset journal titles or other non-MEDLINE journal titles in PubMed)
+2. [LocatorPlus][22], the NLM online catalog and [NLM Catalog][23], an Entrez database
+3. [Serfile][24] may be leased from NLM
+4. [PubMed journals files][25] (contains limited journal information; updated daily)
+5. [NLM Catalog][26] for basic journal information similar to data found in PubMed journals list (available in the [Entrez Utilities][15]; updated daily).
+
+Also see the[ NLM FAQ: Finding NLM® Serials Data and MEDLINE® Indexed Journals][27]. For additional information about MEDLINE/PubMed, see the [MEDLINE/PubMed Resources Guide][28].
+
+[1]: /pubs/factsheets/medline.html
+[2]: http:https://www.ncbi.nlm.nih.gov/pubmed/
+[3]: /databases/databases_oldmedline.html
+[4]: /pubs/factsheets/dif_med_pub.html
+[5]: http:https://www.nlm.nih.gov/news/medlinedata.html
+[6]: http:https://www.nlm.nih.gov/databases/dtd/medline_characters.html
+[7]: /databases/dtd/
+[8]: http:https://www.nlm.nih.gov/bsd/licensee/data_elements_doc.html
+[9]: /bsd/licensee/medpmmenu.html
+[10]: /bsd/licensee/medline_maintenance.html
+[11]: http:https://mbr.nlm.nih.gov/
+[12]: /bsd/sample_records_avail.html
+[13]: http:https://www.nlm.nih.gov/databases/license/license.html
+[14]: /databases/download.html
+[15]: http:https://www.ncbi.nlm.nih.gov/books/NBK25500
+[16]: /bsd/licensee/
+[17]: /pubs/techbull/tb.html
+[18]: http:https://www.nlm.nih.gov/listserv/emaillists.html
+[19]: /mesh/meshhome.html
+[20]: /hmd/indexcat/indexcatxml.html
+[21]: /tsd/serials/lsiou.html
+[22]: http:https://locatorplus.gov/
+[23]: http:https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nlmcatalog
+[24]: /databases/leased.html
+[25]: /bsd/serfile_addedinfo.html
+[26]: http:https://www.ncbi.nlm.nih.gov/nlmcatalog
+[27]: /bsd/journals_database_faq.html
+[28]: /bsd/pmresources.html

licenses/custom/MeSH.md

@@ -0,0 +1,27 @@
+Retrieved from https://www.nlm.nih.gov/mesh/termscon.html on 2015-08-21.
+
+***
+
+# MeSH® Memorandum of Understanding
+
+You should read carefully the following Memorandum of Understanding. Downloading MeSH data through this site indicates your acceptance of the following terms and conditions.
+
+1\. MeSH Subject Authority File
+
+MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. Several MeSH files are available via FTP and have online documentation. MeSH is updated annually and users of this information are encouraged to obtain the new year's data. The data are generally available by mid-November of the preceding year.
+
+2\. Terms and conditions of use
+
+No license is required to obtain the data via FTP. Use of this data is subject to the following restrictions and by obtaining a copy of the data, the user is understood to abide by these conditions:
+
+: a). If the use is not personal, (1) the U.S. National Library of Medicine must be identified as the creator, maintainer, and provider of the data; (2) the version of the data must be clearly stated by MeSH year, e.g., 1997 MeSH; and (3) if any modification is made in the content of the file, this must be stated, along with a description of the modifications.
+
+b). Neither the United States Government, nor any of its agencies, contractors, subcontractors or employees makes any warranties, expressed or implied, with respect to data contained in the database, and, furthermore, assumes no legal liability for any party's use, or the results of such use, of any part of the database.
+
+c). You will not assert any proprietary rights to any portion of the database, or represent the database or any part thereof to anyone as other than a United States Government database.
+
+d). The MeSH data carry an international copyright outside the United States, its Territories or Possessions. These terms and conditions are in effect as long as the user retains any of the MeSH data obtained from this site.
+
+3\. Availability
+
+The data are available to all requesters, both within and outside the United States. There is no charge for obtaining the file. Users are required to complete an online registration form before receiving the data.