It is vital that a community uses the same vocabulary so as to :
1) understand each other
2) convert what we understand in computer objects
3) share these objects
Three types of standards allow a representation, description and reporting experimental data.
- Minimum information basic checklists
- Semantics: classifications, terminologies and relationships between all terms that is to say ontologies
- Syntax: exchange formats
Here a list of the recommended standards for the community :
- AMIS, the Article Minimum Information Standard : this standard describes for each experiment the mandatory (and useful) information that should be mentioned in literature articles. For more information : http://www.aniseed.cnrs.fr/AMIS.php
- MISFISHIE, the Minimum Information Specification For In Situ Hybridization and Immunohistochemistry experiments. For more information : http://scgap.systemsbiology.net/standards/misfishie/
- MISRRA, the Minimum Information Specification for Regulatory Region Analysis. Article in process.
- cDNA clone : Genbank ID ; Library ID
- Gene name : Access to the preliminary document proposing some rules to name various genome features.
- Anatomical ontology : ciona_intestinalis.obo ; halocynthia_roretzi.obo ; botryllus_schlosseri.obo
- Gene ontology
- Sequence ontology
- Evidence Code ontology : encode information about why we believe certain assertions in a database, the source of those assertions, and the degree of confidence scientists hold in those assertions (e.g. « inferred from morpholino experiment » ; « inferred from computational analysis » ; « inferred from the curator »). Here the latest version of the obo file : http://bioportal.bioontology.org/ontologies/1012
- PATO : ontology of phenotypic qualities
- Chebi : qualifier of chemical compounds