It is crucial that a community uses the same vocabulary so as to :
- understand each other
- convert what we understand in computer objects
- share these objects
Standards allow the data (descriptions of biological entities, eg, genes, targets and their measures, eg, intensity, location) to be shared, accompanied by a sufficient number of experimental data (annotation =) (ie from the study materials, technology and measurement types, etc.).
Three types of standards allow a representation, description and reporting experimental data :
- Minimum information basic checklists
- Semantics: classifications, terminologies and relationships between all terms (= ontologies)
- Syntax: nomenclature and exchange formats
Here a list of the recommended standards for the community
AMIS, the Article Minimum Information Standard describes for each experiment the mandatory (and useful) information that should be mentioned in literature articles.
This standard was published in the first ANISEED paper in 2010
MISRRA, the Minimum Information Specification for Regulatory Region Analysis.
A set of nomenclature rules, consensual within the community, was defined for predicted genes, pseudogenes, transcripts, operons, transcriptional cis-regulatory regions, transposable elements, and transgenic constructs. In addition, the document proposes guidelines for naming transgenic and mutant lines.
These guidelines was published in Genesis, in 2015
TUNICATE ANATOMY AND DEVELOPMENT ONTOLOGY
Anatomical and developmental ontologies was set up for some Tunicate species :
- A precise ontology was defined for Ciona intestinalis. The strong developmental conservation between Ciona intestinalis and Ciona savignyi, Phallusia mammillata, Halocynthia roretzi, Boltenia villosa was used to create parallel tentative embryonic and adult anatomical ontologies for these species. Because of the phylogenetic proximity of C. savignyi and P. mammillata to C. intestinalis, their ontologies were inferred to be identical to those of Ciona intestinalis. The ontologies of the more distantly related H. roretzi and B. villosas lightly deviate from those of Ciona.
These ontologies are described in Tassy et al. 2010.
- Botryllus schlosseri : the first ontology for anatomy and asexual development (blastogenesis) of a bilaterian, the colonial tunicate Botryllus schlosseri was set up in 2014. This ontology is described in Manni et al. 2014.
- Ciona robusta : a new version of the ontology of Ciona robusta is described in Manni et al. 2020, submitted. You can download the version of the obo file (08/05/2020) here.
All these ontologies can be downloaded for each species in the ANISEED download section and browsed here.
If you have any suggestions to improve ontologies, please contact us : firstname.lastname@example.org
Gene Ontology (GO) is used to annotate tunicate gene models in ANISEED
Sequence Ontology (SO) is used to define the sequence features used in biological sequence annotation. This controlled vocabulary is used in ANISEED.
EVIDENCE AND CONCLUSION ONTOLOGY
This ontology is used to 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 »).
It is partially used in ANISEED (not well implemented yet).
PHENOTYPIC QUALITY ONTOLOGY
This ontology describing phenotype can be used in conjunction with other ontologies such as GO or anatomical ontologies to refer to phenotypes. Examples of qualities are red, ectopic, high temperature, fused, small, edematous and arrested.
It is not yet used by the community.
CHEMICAL ENTITIES OF BIOLOGICAL INTEREST ONTOLOGY
Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds.
It is not yet used by the community.