D7.9

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D7.9: Report on existing metadata standards, and proposals for new vocabularies

Part of Task_7.4

Builds on File:Report on existing standards.pdf, Existing metadata services, Provenance, D3.5.

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Much important work is being undertaken by the PDB's Validation Task Forces. Our aim is to complement this work, not to compete with it. See especially Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop.

D3.5 reported a "prototype deposition and archiving system for structural models obtained through integrative/hybrid methods" at https://pdb-dev.wwpdb.org, and partner EMBL-EBI has appealed to the community for more depositions into this database.

Gap analysis

  • Current workflows in Structural Biology may not be properly described in an unambiguous manner due to the lack of appropriate metadata standards specifying them (M6.3 report).
  • there is no agreed ontology for the primary data processing, either at the level of integrated studies combining different technologies or even at the single technique level (M6.3 report).
  • Metadata about experimental conditions are often incomplete
  • as a result of this, the chain of custody from sample to publication is often broken at several points
  • takeup of mmCIF has been slow but West-Life has catalyzed some progress described below.

CWL

Some work at CSIC.

mmCIF

The PDB-REDO databank now stores mmCIF files and the PDB_REDO service reads and writes mmCIF, and version 8 will use mmCIF internally. DipCheck now accepts mmCIF input, and ARP/WARP accepts mmCIF for ligands but not proteins.

Relevant Categories

audit_group: audit_author,pdbx_version citation software (87.4%), _software.classification pdbx_construct (0%) _entity.id

See also: M7.9 M32 Existing services updated to existing data types

Alexandre writes "we are working with the integrative modelling task force to facilitate deposition of integrative model (in mmCIF) into the new PDB site for those: https://pdb-dev.wwpdb.org

The first HADDOCK model has been deposited (see last entry on the page - there is not yet a landing page per entry)! But this was a lot of manual effort. And the mmCIF definition for integrative models is very much work in progress. Many new additions were made because of our involvement to support HADDOCK data.

See: https://github.com/ihmwg

Mikael is just back from a visit to Andrej Sali’s lab and the RCSB where he discussion further how we can facilitate integrative models deposition. Our aim is to populate as much as possible of a mmCIF file with the info coming out of HADDOCK.

"

PROV-O

Evidence and Conclusion Ontology

References

https://link.springer.com/chapter/10.1007/978-3-319-58068-5_20

https://www-internal.psfc.mit.edu/research/alcator/pubs/APS/APS2014/Greenwald_APS-poster_%202014.pdf and https://mpo.psfc.mit.edu/about.html

https://www.researchgate.net/publication/229019700_Scientific_workflow_provenance_metadata_management_using_an_RDBMS

https://f1000research.com/posters/6-1547#