Controlled Vocabularies and Ontologies

Help Index > Controlled Vocabularies and Ontologies

SysMO-DB recommends that consortium members use identifiers from public databases and terms from community ontologies wherever possible when describing and annotating data and models. The following table shows the resources available for annotation by biological object category. These are the resources recommended by SysMO-DB and also represent the most commonly used in the SysMO consortium.

Entity Resource Example ID Database URL MIRIAM URN
Protein UNIPROT P23470 http://www.ebi.uniprot.org urn:miriam:uniprot
Chemical ChEBI CHEBI:17234 http://www.ebi.ac.uk/chebi/ urn:miriam:obo.chebi
Chemical KEGG Compund C0003 http://www.genome.jp/kegg/ligand.html urn:miriam:kegg.compound
Chemical PubChem CID:24749
http://pubchem.ncbi.nlm.nih.gov/
urn:miriam:pubchem.compound
Reaction Kinetics SABIO-RK 20936 http://sabio.h-its.org/ urn:miriam:sabiork.reaction
Enzymes Enzyme Nomenclature (EC) IntEnz EC 1.14.13.39 http://www.ebi.ac.uk/intenz/ urn:miriam:ec-code
Pathways KEGG Pathways map00480 http://www.genome.jp/kegg/pathway.html urn:miriam:kegg.pathway
Cellular Location Gene Ontology GO:0016020 http://www.geneontology.org/ urn:miriam:obo.go
Molecular Function Gene Ontology GO:0004857 http://www.geneontology.org/ urn:miriam:obo.go
Biological Process Gene Ontology GO:0071581 http://www.geneontology.org/ urn:miriam:obo.go
Literature PubMed PMID:19112082 http://www.ncbi.nlm.nih.gov/pubmed/ urn:miriam:pubmed
Model Descriptions Systems Biology Ontology SBO:0000244 http://www.ebi.ac.uk/sbo/ urn:miriam:biomodels.sbo

Assistance with Data and Models Annotation

Accessing and navigating these resources can be difficult and time-consuming for large data sets. SysMO-DB provide tools to make data and model annotation easier.

RightField

RightField (http://www.rightfield.org.uk) allows the easy annotation of excel spreadsheet data with terms from community ontologies. Relevant ranges of ontology terms can be embedded into spreadsheets in specific cells as simple drop-down lists. This allows consistent and standards-compliant annotation without the need to browse or navigate the ontologies.
Multiple ontologies can be used in the same spreadsheet, and the sources of each term and the version of each ontology is automatically collected and recorded.
A collection of SysMO templates have already been RightField-enabled. These templates are available for download from the templates page and from the SysMO-DB project in the SEEK.

JWS OneStop

OneStop assists with model annotation and publishing. It is a one-stop-shop for producing a MIRIAM-compliant, annotated model in SBML. OneStop extracts the names used for species and reactions in an uploaded model and uses these names to search public databases for the official terms and MIRIAM identifiers. It uses the Semantic SBML web service (http://semanticsbml.org/) for searching and returns a list of possible matches that the modellers can select from. This ensures the accuracy of each annotation whilst providing an easy mechanism for identifying possible matches.
In addition to annotations, OneStop also provides editing and validation functionality as well as automatically exporting models in SBGN.


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