Transitioning Biocyc to a Subscription Model

Transitioning BioCyc to a Subscription Model

Peter D. Karp ecocyc.org SRI International biocyc.org metacyc.org

© 2014 SRI International BioCyc.org Collection of 9,300 Pathway/Genome Databases •Pathway/Genome Database (PGDB) – combines information about – Pathways, reactions, substrates – Enzymes, transporters – Genes, replicons – Transcription factors/sites, promoters, operons

•Tier 1: Highly curated PGDBs – MetaCyc, HumanCyc, YeastCyc – EcoCyc -- Escherichia coli K-12 – AraCyc – Arabidopsis thaliana

•Tier 2: Moderately curated -- 44 PGDBs – Bacillus subtilis, Mycobacterium tuberculosis

•Tier 3: Computationally-derived DBs

• Access to an extremely wide range of curated and computationally predicted information: – Genes and proteins – Metabolic pathways, reactions, metabolites – Regulatory networks • Gene expression data analysis • Metabolomics data analysis • Execute metabolic models • Metabolic route searches • Comparative analysis

Database Organism Organization Publications Curated From MetaCyc Multiorganism SRI 51,000 EcoCyc E. coli SRI 32,000 BsubCyc B. subtilis SRI 4,000 HumanCyc H. sapiens SRI AraCyc A. thaliana TAIR/Carnegie 4,100 Institution YeastCyc S. cerevisiae SGD/SRI 980 MouseCyc M. musculus MGD/Jackson Laboratory

http://biocyc.org/otherpgdbs.shtml

Computational Inferences

Predict metabolic reactions NIH Predict operons Predict transport reactions Compute orthologs RefSeq Predict metabolic pathways Compute Pfam domains Predict pathway hole fillers Curation PGDB

Regulatory data Database links [regtransbase] Organism phenotype data Subcellular locations [psortdb] Gene essentiality data Phenotype microarray data GO terms [uniprot] Protein features [uniprot]

• Gene functions • Metabolic pathways, reactions, metabolites • Regulatory interactions

• EcoCyc grant from NIH/NIGMS (3 FTE curators) • MetaCyc grant from NIH/NIGMS (1 FTE curator) • Support curation of two of our 9,600 databases

• Additional revenues will let us curate additional databases

• Gov’t supported databases remain free/open • Other databases accessible via subscription • Subscriptions available to individuals and institutions • Institutional subscription price depends upon usage level

• Phoenix Bioinformatics provides us with sales, marketing, and paywall services

© 2014 SRI International • NL-understanding problem is 60 years old • Lots of progress, but error rates are unacceptable (18%, 24%, 45%) • Info extraction software typically extracts narrow slivers of info • Cannot arbitrate among conflicts in the literature • Some evidence that info-extraction software can speed curation

• Number of extracted datatypes • Number of database fields • Amount of meta-data (evidence codes) • Amount of interpretation and synthesis • Authoring of mini-reviews • End-uses of information (metabolic modeling)