Guide to Character Annotation
Genus-differentia definitions
Term definitions in the teleost anatomy ontology (TAO) take the form of genus-differentia definitions: B is an A that has X.
The term B is defined by its membership in higher category A and distinguished from its sibling terms by characteristic X. The following are examples of genus-differentia definitions in the TAO:
- Antorbital: Dermal bone that is located on the anterior margin of the infraorbital series, dorsal to the first infraorbital and lateral to the nasal bone.
- Dentary: Dermal bone that forms the anterolateral part of the lower jaw.
In example 1, the definition mentions the parent dermal bone of the term antorbital, followed by the characteristics that differentiate antorbital from all other dermal bones.
Post-composed terms (terms created on-the-fly at the time of annotation) take the form of genus-differentia definitions (see Character Type 5, below).
Evidence Codes
We record phenotype descriptions as properties of species, and annotations are assigned one of three evidence codes based on the level of evidence given by an author for phenotype observations. These specimen evidence codes are in an Evidence Codes Ontology that was developed by the broader biological community (see http://obofoundry.org/cgi-bin/detail.cgi?id=evidence_code). We have added evidence codes to this ontology, and we use the following in order below from strong to weak evidence.
Inferred from Voucher Specimen (IVS)
Used when an annotation is made on the basis of a phenotype description for a species or higher level group that is given by an author who explicitly references an observation of a voucher specimen(s). Voucher specimens are defined as those specimens with permanent museum catalog numbers. Thus it would be possible for a person to examine this particular specimen and observe the annotated phenotype.
Traceable Author Statement (TAS)
The TAS evidence code covers author statements that are attributed to a cited source. Typically this type of information comes from review articles. Material from the introductions and discussion sections of non-review papers may also be suitable if another reference is cited as the source of experimental work or analysis. When annotating with this code the curator should use caution and be aware that authors often cite papers dealing with experiments that were performed in organisms different from the one being discussed in the paper at hand. Thus a problem with the TAS code is that it may turn out from following up the references in the paper that no experiments were performed on the gene in the organism actually being characterized in the primary paper. For this reason we recommend (when time and resources allow) that curators track down the cited paper and annotate directly from the experimental paper using the appropriate experimental evidence code. When this is not possible and it is necessary to annotate from reviews, the TAS code is the appropriate code to use for statements that are associated with a cited reference. Once an annotation has been made to a given term using an experimental evidence code, we recommend removing any annotations made to the same term using the TAS evidence code.
Nontraceable Author Statement (NAS)
The NAS evidence code should be used in all cases where the author makes a statement that a curator wants to capture but for which there are neither results presented nor a specific reference cited in the source used to make the annotation. The source of the information may be peer reviewed papers, textbooks, database records or vouchered specimens.
Character types
The following are examples of character types commonly enountered in the systematic literature and how we annotate them using the EQ model in Phenote. Abbreviations: E, entity; Q, quality, AE, additional entity, C, count.
Presence/absence characters
E: pectoral fin, Q: present E: pectoral fin, Q: absent
Note that “presence” is the parent term for absent and present, and should not be used in annotations.
Characters using monadic qualities
Monadic qualities are those that exist in a single entity, such as shape, and do not require another entity. For example, annotation of “sigmoid-shaped supraorbital bone” is entered as:
E: supraorbital, Q: sigmoid
Characters using relational qualities
Relational qualities are those that exist in an entity but require an additional entity in order to exist. For example, annotation of “parietal fused with supraoccipital” is entered as:
E: parietal, Q: fused with, AE: supraoccipital
Meristic data
Characters involving counts of entities are annotated using the “count” quality. Values for counts are entered in the “count” field. Note that ranges and lower or upper bounds can be recorded:
E: vertebra, Q: count, C: 33 E: vertebra, Q: count, C: 34-38 E: vertebra, Q: count, C: >38
Could say here: Relationships across taxa between individual entities in a meristic series (e.g. vertebra 4 in a zebrafish vs. vertebra 4 in an eel), are not necessarily homologous. These can be handled in several ways, and we will discuss them here.
Post-composition of entity term
Some terms can be post-composed at the time of annotation rather than pre-composed within the ontology. Post-composed terms are created in Phenote and follow genus-differentia definitions. Unlike pre-composed terms, post-composed terms do not have an ID.
To post-compose the entity “branched dorsal-fin ray”, type “dorsal fin ray” in the Entity field, click the “Comp” button, select “has_quality” in the relationship field, and type “branched” in differentia field. Click OK. UPDATE SCREENSHOT
The post-composed term appears as
E: dorsal fin lepidotrichium ^has_quality(branched)
Post-composition using spatial terms
The Spatial Ontology is used to post-compose terms related to bone margins, surfaces, or regions. For example, the character “anterior margin of frontal bone serrate” is post-composed as follows:
Type “anterior margin” in the entity field and click the “comp” button. Note that the term anterior margin is expanded in the Post Composition window because “anterior margin” is a pre-coordinated term in the Spatial Ontology. Click the + button to add relationship = part_of and differentia = frontal bone. Click the OK button.
The post-composed term for anterior margin of frontal appears as: anatomical margin^has_position(anterior)^part_of(frontal bone)
Size qualities
Because size qualities are monadic terms, comparison of size of one bone relative to another requires post-composition of the size quality. For example, the character “frontal length greater than parietal length” is entered as:
E: frontal Q*: increased length, relative_to partietal *To post-compose the size quality, type ‘increased length’ in the quality field and click “comp” button. Select ‘relative_to’ in the relationship field and type ‘parietal’ in the differentia field. click OK.
Size qualities with ratio
For the characters in which a proportion or ratio is given in relating the length of one bone to another, the value of ratio is recorded. For example: Length of infraorbital 2: (0) over twice as long as infraorbital 1; (1) less than twice as long as infraorbital 1. This would be indicated in Phenote as follows:
E: infraorbital 2, Q*: increased length, relative_to: infraorbital 1, Measurement: >2, Unit: ratio E1: Infraorbital 2, Q*: decreased length, relative_to: infraorbital 1, Measurement: <2, Unit: ratio *post-composition
