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Re-curation Guidelines

These guidelines were originally written for the re-curation of several NeuroMMSig subgraphs in the Alzheimer's Disease Knowledge Assembly during the Human Brain Pharmacome project, but may be generally applicable to other BEL scripts as well.

Code supporting this workflow can be found at https://github.com/pybel/pybel-git and the accompanying manuscript can be cited as [1]:

[1]Hoyt, C. T., et al (2019). Re-curation and Rational Enrichment of Knowledge Graphs in Biological Expression Language. bioRxiv, 536409.

Normalizing Entities

Chemicals

  1. Normalize chemical entities to preferred namespaces (ChEBI, ChEBML, PubChem) whenever possible. MeSH is explicitly discouraged because it is difficult to look up their structures as SMILES or InChI, even with resolving services like UniChem
  2. Formalize knowledge about chemicals that have not yet been encoded in ChEBI (such as Selventa chemicals [SCHEM], the BELIEF chemical namespaces, etc.), drawing from other public resources (PubChem, MeSH, CAS, ChEMBL, UniChem, BridgeDB, ChemSpider, etc.) whenever possible

Protein Complexes and Families

FamPlex has emerged as a resource that maps families and protein complexes (including the Selventa mappings SFAM and SCOMP as well as other widely used namespaces like PFAM and InterPro).

  1. Normalize all entities to FamPlex
  2. Formalize knowledge about new families by making a pull request to FamPlex. See: https://github.com/sorgerlab/famplex#contributing

Other Entities

We are also building a terminology at https://github.com/pharmacome/terminology. This should not be done lightly, so see its contribution guidelines and rules before making a pull request.

Checking Correctness

  • If statement can be asserted from the given evidence, add the annotation SET Confidence = "High"
  • If the statement is wrong, fix it and add the annotation SET Confidence = "Medium"
  • If it's not clear what BEL should represent the biology, add SET Confidence = "Low" for later discussion
  • If the evidence string contains no reasonable biological knowledge/is nonsense, delete it and the related statements entirely. It's okay to remove BEL statements that are not supported.

Finalization

After all relevant statements have been checked for correctness, the curation leader will check all statements with SET Confidence = "High" or SET Confidence = "Medium" and change to SET Confidence = "Very High" if they agree. If they do not agree, they will fix it themselves.