Controlled Vocabularies and Ontologies

This guide refers to SEEK, but is also relevant for FAIRDOMHUB, which is an instance of SEEK.

We recommend SEEK users 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 represent the most commonly used within System Biology.


SEEK documentation is a community driven activity, and we are always looking to expand. If you have any modifications you want to make to the list please send requests, or feedback to

Entity Resource Example ID Database URL MIRIAM URN
Protein UNIPROT P23470 urn:miriam:uniprot
Chemical ChEBI CHEBI:17234 urn:miriam:obo.chebi
Chemical KEGG Compund C0003 urn:miriam:kegg.compound
Chemical PubChem CID:24749
Reaction Kinetics SABIO-RK 20936 urn:miriam:sabiork.reaction
Enzymes Enzyme Nomenclature (EC) IntEnz EC urn:miriam:ec-code
Pathways KEGG Pathways map00480 urn:miriam:kegg.pathway
Cellular Location Gene Ontology GO:0016020 urn:miriam:obo.go
Molecular Function Gene Ontology GO:0004857 urn:miriam:obo.go
Biological Process Gene Ontology GO:0071581 urn:miriam:obo.go
Literature PubMed PMID:19112082 urn:miriam:pubmed
Model Descriptions Systems Biology Ontology SBO:0000244 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 ( 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 ( 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.