BioModels projects: q-bio 2017

BioModels to be annotated

Huarat 2016
ArnS, a kinase involved in starvation-induced archaellum expression (2016) Molecular Microbiology
BioModels page; paper; supporting info

Talemi 2016
Systems Level Analysis of the Yeast Osmo-Stat (2016) Scientific Reports
BioModels page; paper; supporting info; Copasi file (zipped)

Barr 2017
DNA damage during S-phase mediates the proliferation-quiescence decision in the subsequent G1 via p21 expression (2017) Nature Communications
BioModels page; paper; supporting info; Copasi file (zipped)

Validation using Copasi

For help, see the User Manual. Our example mode is BIOMD0000000009.

Annotation spreadsheets

To enable collaborative annotation, I have extracted the models to Google Spreadsheets. Access the spreadsheet for your model here: http://bit.do/qbio2017.

For examples of completed spreadsheets, see http://bit.do/MCB315BioModels.

Annotation databases

Qualifiers

These specify the relationship between the element of the model and the entry in the database. For Models, common qualifiers are is, isDerivedFrom, isDescribedBy, isInstanceOf, hasInstance. For Biological Entities, common qualifiers include hasPart, is, isEncodedBy, isHomologTo, isPartOf, isVersionOf, hasTaxon.
For an brief guide, see here. For a complete list, see here.

Proteins

UniProt; guide
The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. Besides amino acid sequence and a description, it also provides taxonomic data and citation information.

Interpro; guide
InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.

Small molecules

ChEBI; guide
Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds.

KEGG Compound
KEGG compound contains our knowledge on the universe of chemical substances that are relevant to life.

Genes and transcripts

NCBI Gene; guide
Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.

Reactions

Gene Ontology; guide
The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism.

KEGG Reaction
KEGG reaction contains our knowledge on the universe of reactions that are relevant to life.

Reactome
The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology.

Compartments

Gene Ontology

Publications

Pubmed
PubMed comprises more than 26 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

Organisms

UniProt Taxonomy
Organisms are classified in a hierarchical tree structure. Our taxonomy database contains every node (taxon) of the tree.

Tissues

BRENDA Tissue Ontology
BTO provides terms, classifications, and definitions of tissues, organs, anatomical structures, plant parts, cell cultures, cell types, and cell lines of organisms from all taxonomic groups (animals, plants, fungis, protozoon) as enzyme sources. The information is connected to the functional data in the BRENDA enzyme information system.

Biological processes

Gene Ontology
The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism.