SPOKE Source Licenses

Most sources are listed along with their licensing information in Table 4 of Himmelstein et al. eLife (2017):

Table 4
The 29 public data resources integrated to construct Hetionet v1.0.

Components notes which types of nodes and edges in Hetionet v1.0 derived from the resource (as per the abbreviations in Table 1 and 2). Cat. notes the general category of license (Himmelstein et al., 2015i). Category 1 refers to United States government works that we deemed were not subject to copyright. Category 2 refers to resources with licenses that allow use, redistribution, and modification (although some restrictions may still exist). The subset of category 2 licenses that we deemed to meet the the Open Definition are denoted with OD. Category 4 refers to resources without a license, hence with all rights reserved. References provides Research Resource Identifiers as well as citations to resource publications and related Project Rephetio materials. For information on license provenance, institutional affiliations, and funding for each resource, see the online table.

A few newer edge types derived from sources already in Table 4 have been added in green.
Resources no longer used and edge types no longer in SPOKE are shown in brown.
Pending or in-progress items are in gold.

ResourceComponentsLicense Cat.References
Entrez GeneGcustom1 RRID:SCR_002473 (Maglott et al., 2011; Himmelstein et al., 2015h; Himmelstein, 2016l)
LabeledInCtD, CpDcustom1 RRID:SCR_015667 (Khare et al., 2014; Khare et al., 2015; Himmelstein and Khare, 2015s)
MEDLINEDlA, DpS, DrDcustom1 RRID:SCR_002185 (Himmelstein and Pankov, 2015a; Himmelstein, 2016u)
MeSHScustom1 RRID:SCR_004750 (Himmelstein and Pankov, 2015a; Himmelstein, 2016h)
Pathway Interaction DatabasePW, GpPW1 RRID:SCR_006866 (Schaefer et al., 2009; Pico and Himmelstein, 2015; Himmelstein and Pico, 2016a)
Disease OntologyD
DcD, DiD
CC BY 3.02OD RRID:SCR_000476 (Schriml et al., 2012; Kibbe et al., 2015; Himmelstein and Li, 2015d; Himmelstein, 2016g)
DISEASESDaGCC BY 4.02OD RRID:SCR_015664 (Himmelstein and Jensen, 2015l; Himmelstein and Jensen, 2016c; Pletscher-Frankild et al., 2015)
DrugCentralPC, PCiC, CbG, CbP (now also CtD)CC BY 4.02OD RRID:SCR_015663 (Ursu et al., 2017; Himmelstein et al., 2016d)
Gene OntologyBP, CC, MF, GpBP, GpCC, GpMFCC BY 4.02OD RRID:SCR_002811 (Ashburner et al., 2000; Huntley et al., 2015; Himmelstein et al., 2015g; Himmelstein et al., 2015f)
GWAS CatalogDaGcustom2OD RRID:SCR_012745 (Himmelstein and Baranzini, 2016b; MacArthur et al., 2017; Himmelstein, 2015h; Himmelstein et al., 2015v)
ReactomePW, GpPWcustom2OD RRID:SCR_003485 (Fabregat et al., 2016; Cerami et al., 2011; Pico and Himmelstein, 2015; Himmelstein and Pico, 2016a)
LINCS L1000CdG, CuG, KGdG, KGuG, OGdG, OPuG, GPdG, GPuG, Gr→Gcustom2OD (Himmelstein and Chung, 2015q; Himmelstein et al., 2016k; Himmelstein, 2015k)
TISSUESAeGCC BY 4.02OD RRID:SCR_015665 (Santos et al., 2015; Himmelstein and Jensen, 2015g; Himmelstein and Jensen, 2015h)
AcA, AiA, ApA
CC BY 3.02OD RRID:SCR_010668 (Mungall et al., 2012; Malladi et al., 2015; Himmelstein, 2016m)
WikiPathwaysPW, GpPWCC BY 3.0/custom2OD RRID:SCR_002134 (Kutmon et al., 2016; Pico et al., 2008; Pico and Himmelstein, 2015; Himmelstein and Pico, 2016a)
BindingDBCbG, CbPmixed CC BY 3.0 and CC BY-SA 3.02OD RRID:SCR_000390 (Chen et al., 2001; Gilson et al., 2016; Himmelstein and Gilson, 2015i; Himmelstein et al., 2015d)
DisGeNETDaGODbL2OD RRID:SCR_006178 (Himmelstein, 2015f; Himmelstein and Piñero, 2016d; Piñero et al., 2015; Piñero et al., 2017)
DrugBankC, CbG, CrCcustom2 RRID:SCR_002700 (Law et al., 2014; Himmelstein, 2015b; Himmelstein, 2016i; Himmelstein et al., 2016r)
MEDICtD, CpDCC BY-NC-SA 3.02 RRID:SCR_015668 (Himmelstein et al., 2015e; Wei et al., 2013)
PREDICTCtD, CpDCC BY-NC-SA 3.02 (Gottlieb et al., 2011; Himmelstein et al., 2015e)
SIDERSE, CcSECC BY-NC-SA 4.02 RRID:SCR_004321 (Kuhn et al., 2016; Himmelstein, 2015c; Himmelstein, 2016j)
BgeeAeG, AdG, AuG4 RRID:SCR_002028 (Himmelstein et al., 2016f; Himmelstein and Bastian, 2015e; Himmelstein and Bastian, 2015f; Bastian et al., 2008)
DOAFDaG4 RRID:SCR_015666 (Himmelstein, 2015g; Himmelstein, 2016s; Xu et al., 2012)
ehrlinkCtD, CpD4 (McCoy et al., 2012; Himmelstein, 2015j)
Evolutionary Rate CovariationGcG4 RRID:SCR_015669 (Priedigkeit et al., 2015; Himmelstein and Partha, 2015r; Himmelstein, 2016w)
hetio-dagGiG4 (Himmelstein and Baranzini, 2015a; Himmelstein et al., 2015z; Himmelstein and Baranzini, 2016e)
Incomplete InteractomeGiG4 (Himmelstein et al., 2015z; Himmelstein and Baranzini, 2016e; Menche et al., 2015; Himmelstein, 2015a)
Human Interactome DatabaseGiG4 RRID:SCR_015670 (Himmelstein et al., 2015z; Himmelstein and Baranzini, 2016e; Rual et al., 2005; Venkatesan et al., 2009; Yu et al., 2011; Rolland et al., 2014)
STARGEODdG, DuG4 (Himmelstein et al., 2015a; Himmelstein et al., 2016j; Hadley et al., 2017)

Below are new sources added since v1.0. Some are less clear than others about their terms of data usage. Some are free for noncommercial use only.

ResourceComponentsLicense Cat.References
ChEMBLC, CbP, CtD CC Attribution-ShareAlike 3.0 Unported http://chembl.blogspot.com/2010/10/chembl-licensing.html
UniProtP, GeP CC BY 4.02OD https://www.uniprot.org/help/license
STRINGPiP CC BY 4.02OD https://string-db.org/cgi/access.pl?footer_active_subpage=licensing
Online Mendelian Inheritance in Man (OMIM)DaG https://www.omim.org/help/agreement
FooDBF, N, FcC, FcN http://foodb.ca/about
CIViC (Clinical Interpretations of Variants in Cancer)CamG CC0 1.0 Universal https://civicdb.org/releases
Genomics of Drug Sensitivity in Cancer (GDSC)CamG CC Attribution-NonCommercial-NoDerivs 2.5?? https://www.cancerrxgene.org/legal
ClinicalTrials.govCamG (and via ChEMBL, CtD) https://clinicaltrials.gov/ct2/about-site/terms-conditions
Human Protein Atlas ACT, ACTeP CC Attribution-ShareAlike 3.0 International https://www.proteinatlas.org/about/licence
Cell Ontology CT CC BY 3.02OD http://obofoundry.org/ontology/cl.html
Kyoto Encyclopedia of Genes and Genomes (KEGG) C, EC, O, PW, R, ECcR, OiEC, OiPW, PWiEC, PWcPW, PWiPW, PiEC, RcC, RpC free for academic use, with academic service providers requested to obtain an academic FTP subscription https://www.genome.jp/kegg/legal.html
MetaCyc EC, O, PW, R, ECcR, OiEC, OiPW, PWiEC, PWcPW, PWiPW, PiEC, RcC, RpC EcoCyc and MetaCyc free (other BioCyc data requires subscription) https://biocyc.org/download.shtml
PATRIC OiEC, OiPW freely available https://docs.patricbrc.org/about.html
NCBI Taxonomy OiO, OcO no restrictions on molecular data https://www.ncbi.nlm.nih.gov/home/about/policies/
PathoPhenoDB OcD data and source code freely available https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6546783/
Pfam PF, PD, PDmPF CC0 http://pfam.xfam.org/about
InterPro PDpP all information freely available https://www.ebi.ac.uk/interpro/about/interpro/
Protein Common Interface Database (ProtCID) CbPD, PiP, PDiPD custom (private communication) http://dunbrack2.fccc.edu/ProtCiD/About.aspx