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.
| Resource | Components | License | Cat. | References |
|---|---|---|---|---|
| Entrez Gene | G | custom | 1 | RRID:SCR_002473 (Maglott et al., 2011; Himmelstein et al., 2015h; Himmelstein, 2016l) |
| LabeledIn | CtD, CpD | custom | 1 | RRID:SCR_015667 (Khare et al., 2014; Khare et al., 2015; Himmelstein and Khare, 2015s) |
| MEDLINE | DlA, DpS, DrD | custom | 1 | RRID:SCR_002185 (Himmelstein and Pankov, 2015a; Himmelstein, 2016u) |
| MeSH | S | custom | 1 | RRID:SCR_004750 (Himmelstein and Pankov, 2015a; Himmelstein, 2016h) |
| Pathway Interaction Database | PW, GpPW | 1 | RRID:SCR_006866 (Schaefer et al., 2009; Pico and Himmelstein, 2015; Himmelstein and Pico, 2016a) | |
| Disease Ontology | D DcD, DiD | CC BY 3.0 | 2OD | RRID:SCR_000476 (Schriml et al., 2012; Kibbe et al., 2015; Himmelstein and Li, 2015d; Himmelstein, 2016g) |
| DISEASES | DaG | CC BY 4.0 | 2OD | RRID:SCR_015664 (Himmelstein and Jensen, 2015l; Himmelstein and Jensen, 2016c; Pletscher-Frankild et al., 2015) |
| DrugCentral | PC, PCiC, CbG, CbP (now also CtD) | CC BY 4.0 | 2OD | RRID:SCR_015663 (Ursu et al., 2017; Himmelstein et al., 2016d) |
| Gene Ontology | BP, CC, MF, GpBP, GpCC, GpMF | CC BY 4.0 | 2OD | RRID:SCR_002811 (Ashburner et al., 2000; Huntley et al., 2015; Himmelstein et al., 2015g; Himmelstein et al., 2015f) |
| GWAS Catalog | DaG | custom | 2OD | RRID:SCR_012745 (Himmelstein and Baranzini, 2016b; MacArthur et al., 2017; Himmelstein, 2015h; Himmelstein et al., 2015v) |
| Reactome | PW, GpPW | custom | 2OD | RRID:SCR_003485 (Fabregat et al., 2016; Cerami et al., 2011; Pico and Himmelstein, 2015; Himmelstein and Pico, 2016a) |
| LINCS L1000 | CdG, CuG, KGdG, KGuG, OGdG, OPuG, GPdG, GPuG, Gr→G | custom | 2OD | (Himmelstein and Chung, 2015q; Himmelstein et al., 2016k; Himmelstein, 2015k) |
| TISSUES | AeG | CC BY 4.0 | 2OD | RRID:SCR_015665 (Santos et al., 2015; Himmelstein and Jensen, 2015g; Himmelstein and Jensen, 2015h) |
| Uberon | A AcA, AiA, ApA | CC BY 3.0 | 2OD | RRID:SCR_010668 (Mungall et al., 2012; Malladi et al., 2015; Himmelstein, 2016m) |
| WikiPathways | PW, GpPW | CC BY 3.0/custom | 2OD | RRID:SCR_002134 (Kutmon et al., 2016; Pico et al., 2008; Pico and Himmelstein, 2015; Himmelstein and Pico, 2016a) |
| BindingDB | CbG, CbP | mixed CC BY 3.0 and CC BY-SA 3.0 | 2OD | RRID:SCR_000390 (Chen et al., 2001; Gilson et al., 2016; Himmelstein and Gilson, 2015i; Himmelstein et al., 2015d) |
| DisGeNET | DaG | ODbL | 2OD | RRID:SCR_006178 (Himmelstein, 2015f; Himmelstein and Piñero, 2016d; Piñero et al., 2015; Piñero et al., 2017) |
| DrugBank | C, CbG, CrC | custom | 2 | RRID:SCR_002700 (Law et al., 2014; Himmelstein, 2015b; Himmelstein, 2016i; Himmelstein et al., 2016r) |
| MEDI | CtD, CpD | CC BY-NC-SA 3.0 | 2 | RRID:SCR_015668 (Himmelstein et al., 2015e; Wei et al., 2013) |
| PREDICT | CtD, CpD | CC BY-NC-SA 3.0 | 2 | (Gottlieb et al., 2011; Himmelstein et al., 2015e) |
| SIDER | SE, CcSE | CC BY-NC-SA 4.0 | 2 | RRID:SCR_004321 (Kuhn et al., 2016; Himmelstein, 2015c; Himmelstein, 2016j) |
| Bgee | AeG, AdG, AuG | 4 | RRID:SCR_002028 (Himmelstein et al., 2016f; Himmelstein and Bastian, 2015e; Himmelstein and Bastian, 2015f; Bastian et al., 2008) | |
| DOAF | DaG | 4 | RRID:SCR_015666 (Himmelstein, 2015g; Himmelstein, 2016s; Xu et al., 2012) | |
| ehrlink | CtD, CpD | 4 | (McCoy et al., 2012; Himmelstein, 2015j) | |
| Evolutionary Rate Covariation | GcG | 4 | RRID:SCR_015669 (Priedigkeit et al., 2015; Himmelstein and Partha, 2015r; Himmelstein, 2016w) | |
| hetio-dag | GiG | 4 | (Himmelstein and Baranzini, 2015a; Himmelstein et al., 2015z; Himmelstein and Baranzini, 2016e) | |
| Incomplete Interactome | GiG | 4 | (Himmelstein et al., 2015z; Himmelstein and Baranzini, 2016e; Menche et al., 2015; Himmelstein, 2015a) | |
| Human Interactome Database | GiG | 4 | 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) | |
| STARGEO | DdG, DuG | 4 | (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.
| Resource | Components | License | Cat. | References |
|---|---|---|---|---|
| ChEMBL | C, CbP, CtD | CC Attribution-ShareAlike 3.0 Unported | http://chembl.blogspot.com/2010/10/chembl-licensing.html | |
| UniProt | P, GeP | CC BY 4.0 | 2OD | https://www.uniprot.org/help/license |
| STRING | PiP | CC BY 4.0 | 2OD | https://string-db.org/cgi/access.pl?footer_active_subpage=licensing |
| Online Mendelian Inheritance in Man (OMIM) | DaG |
https://www.omim.org/help/agreement
https://www.omim.org/help/copyright |
||
| FooDB | F, 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.gov | CamG (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 3.0 | 2OD | 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 |