Data sources and licences

Anvesh builds its pathways from the published scientific literature and from open, redistributable public data resources. Each shown connection is marked with its source (a research paper, a review or a textbook) and links to it where Anvesh holds one. We gratefully acknowledge the resources below and use them in accordance with their licences.

Openly dedicated to the public domain (CC0 1.0)

  • Reactome — reactome.org
  • WikiPathways — wikipathways.org
  • IntAct (EMBL-EBI) — ebi.ac.uk/intact
  • Biofactoid — biofactoid.org

Creative Commons Attribution 4.0 (CC BY 4.0) — used with attribution

  • UniProt — uniprot.org
  • Gene Ontology (GO) — ontology and gene annotations (GOA) — geneontology.org
  • ChEBI (EMBL-EBI) — ebi.ac.uk/chebi
  • LIPID MAPS — lipidmaps.org
  • SwissLipids — swisslipids.org (SIB Swiss Institute of Bioinformatics; lipid identifiers, classification, subcellular/tissue localisation and literature-cited relationships)
  • Rhea — rhea-db.org (SIB Swiss Institute of Bioinformatics / Expasy; expert-curated biochemical reactions, used to build reaction connections)
  • Plant Reactome — plantreactome.gramene.org — CC BY 3.0 (Gramene / Cold Spring Harbor Laboratory, Oregon State University, Ontario Institute for Cancer Research; curated plant pathway/reaction knowledge)
  • OncoPPi
  • CPTAC data via the NCI Proteomic Data Commons (PDC) — proteomic.datacommons.cancer.gov — represented, not reproduced

BioGRID — MIT License (thebiogrid.org)

Chemical–protein (drug–target) interaction data are used under the MIT License, and BioGRID's interaction records help resolve links to the primary papers. We acknowledge the BioGRID publications:

  • Oughtred R, et al. The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions. Protein Science 2021;30(1):187–200.
  • Stark C, et al. BioGRID: a general repository for interaction datasets. Nucleic Acids Res 2006;34:D535–D539.

SwissLipids — CC BY 4.0 (swisslipids.org)

SwissLipids (swisslipids.org), © SIB Swiss Institute of Bioinformatics, used under the Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/). SwissLipids data were adapted and reformatted for use in Anvesh, and each relationship used is cited to a paper that states it.

Rhea — CC BY 4.0 (rhea-db.org)

Rhea (rhea-db.org), © SIB Swiss Institute of Bioinformatics. All copyrightable parts of the Rhea database are licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) License (https://creativecommons.org/licenses/by/4.0/); Rhea's copyright statement is reproduced here as required. Rhea data were adapted and reformatted for use in Anvesh, and each reaction used is cited to a paper that states it.

Plant Reactome — CC BY 3.0 (plantreactome.gramene.org)

Plant Reactome (plantreactome.gramene.org), from the Gramene project (Cold Spring Harbor Laboratory, Oregon State University and the Ontario Institute for Cancer Research), used under the Creative Commons Attribution 3.0 Unported (CC BY 3.0) License; see the Plant Reactome license (plantreactome.gramene.org/index.php?option=com_content&view=article&id=16&Itemid=253). Plant Reactome curated content was adapted and reformatted for use in Anvesh, and each reaction used is cited to a paper that states it; Anvesh does not redistribute Plant Reactome data under its original names or identifiers.

Public-domain references

  • PubMed / NCBI E-utilities — used within NCBI's usage policy.
  • PubChem — public domain.

Molecule identities are grounded to UniProt (proteins), and to ChEBI and LIPID MAPS (metabolites and lipids). Where a relationship was first suggested by another resource, it is cited to the paper that states it.

Anvesh is an independent research tool. It is not endorsed by, affiliated with, or sponsored by any of the resources listed above.