Guide to Character Annotation

PATO terms used to annotate systematic characters

Below is a simplified graph showing a subset of quality terms from the Phenotype and Trait Ontology (PATO) used to curate systematic characters. Terms in blue represent attribute-level qualities. Qualities are generally divided into those that inhere in a single entity (quality of single physical entities, or "monadic" qualities), and those that inhere in multiple entities (quality of related physical entities, or "relational qualities").

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PATO attribute-level term	Synonyms	Examples of child terms
shape		triangular, lobed, concave, interdigitated
position	placement, location	horizontal, vertical
size*		thin, large, decreased height
structure		porous, non-porous
composition		ligamentous
ossified
cartilaginous
texture		smooth, wrinkled
color
present	present in organism, presence
absent	absent from organism, absence
count	count in organism
relational shape quality*		protruding into
relational spatial quality*		orientation, anterior to, lateral to
relational structural quality*		fused with, overlap with, separated from, in contact with

(*) Relational qualities describe phenotypes between two entities

Character Annotation Examples

The following are examples of character types commonly encountered in the systematic literature and how we annotate them using the EQ model in Phenex. Abbreviations: E, entity; Q, quality, RE, related entity, C, count.

1. Qualities of single physical entities

Qualities of single physical entities are those that exist in a single entity. These qualities include 'shape,' 'size', and 'structure.' For example, “sigmoid-shaped supraorbital bone” is annotated as:

E: supraorbital, Q: sigmoid

2. Qualities of related physical entities

Relational qualities are those that exist between multiple entities. For example, “parietal fused with supraoccipital” is represented as:

E: parietal, Q: fused with, RE: supraoccipital

3. Multiple phenotypes for a single character state

Some characters describe multiple aspects of phenotypic variation in an entity (or entities). These characters are represented with multiple EQ statements. For example, a character state may describe "premaxillary teeth round and multicuspidate." This is represented with the following two phenotypes:

E: premaxillary tooth, Q: round
E: premaxillary tooth, Q: multicuspidate

4. Presence/absence characters

Variation is often reported describing an anatomical entity that is present in some taxa and lacking in others. These characters are annotated using the terms present and absent :

E: pectoral fin, Q: present
E: pectoral fin, Q: absent

Although use of present and absent reflects common usage in language familiar to curators, their use in EQ syntax is illogical because, for example, absent refers to the existence of an entity that is asserted to not exist see PATO wiki for discussion.

If a character describes the presence or absence of a structure located on another entity (for example, teeth present on a particular bone), first check to see whether the structure exists as a term in the TAO before creating a post-composition. For example, "teeth absent on basihyal bone" is annotated as:

E: basihyal tooth, Q: absent

5. Counts

Characters involving counts of entities are annotated using the “count” quality. Values for counts are entered in the “Comment” field(*). Note that ranges and lower or upper bounds are recorded as follows:

E: vertebra, Q: count, Comment: 33
E: vertebra, Q: count, Comment: 34-38
E: vertebra, Q: count, Comment: >38
E: vertebra, Q: count, Comment: ≥48

(*)The "Count" field in Phenex is not currently used because it does not accept ranges or symbols; therefore, please record all numerical values in the Comments field.

6. Annotation involving bone and cartilage terms

Authors sometimes refer to endochondral structures without specifying whether the structure is “bone” or “cartilage.” For example, the convention for a term like “epibranchial 2” or “basibranchial” is that it is composed of bone and when composed of cartilage an author will say “epibranchial 2 cartilage” or “basibranchial cartilage”. However, this is not universally followed and a curator must read the character description and examine associated text and figures to ascertain this. If after reviewing the publication it is still not clear, then the curator can use the “element” term for the structure. In general, the “element” terms should be used sparingly, and only when an author does not indicate whether a structure (e.g. “epibranchial”) is composed of cartilage or bone.

The following are a series of examples demonstrating the use of bone, cartilage, and element terms.

Example 1

Epibranchial 1: (0) present and ossified

E: Epibranchial 1 bone, Q: present

Epibranchial 1: (1) present and cartilaginous

E: Epibranchial 1 cartilage, Q: present

Epibranchial 1: (2) absent

E: Epibranchial 1 cartilage, Q: absent
E: Epibranchial 1 bone, Q: absent

The curator should use both the cartilage and bone terms to annotate state 2 because the author clearly differentiates between the two.

Example 2

Epibranchial 1 (0) present, (0) absent. After careful reading of associated text in the publication, the curator cannot conclude that the author refers to bone or cartilage, and therefore uses "element" term:

E: epibranchial 1 element, Q: present or Q: absent

Example 3

Epibranchial 1 bone: (0) present; (1) absent

E: epibranchial 1 bone; Q: present or Q: absent

Example 4

Epibranchial 1: (0) triangular. After careful reading of associated text in the publication, the curator cannot conclude that the author refers to bone or cartilage, and therefore uses "element" term:

E: epibranchial 1 element, Q: shape

Example 5

Epibranchial number: (0) 3; (1) 4. After careful reading of associated text in the publication, the curator cannot conclude that the author refers to bone or cartilage, and therefore uses "element" term:

E: epibranchial element; Q: count; Comment: 3 or Comment: 4

Example 6

Epibranchial bone number: (0) 3; (1) 4

E: epibranchial bone; Q: count; Comment: 3 or Comment: 4

Contralateral halves of bilaterally paired structures

Terms for the contralateral halves of bilaterally paired structures are created using the in_right_side_of and in_left_side_of relations in a post-composition, where the perspective is from the standpoint of the organism. For example:

E: frontal^in_right_side_of(body), Q: fused with, RE: frontal^in_left_side_of(body).

Creating or refining terms by post-composition

Often times the need arises to create a new term at the time of annotation ("post-composition"), rather than requesting that the new term is formally added to the ontology. Such cases typically arise when annotating the presence of processes on bones. In some cases a more granular term is required than is already present in the ontology, whether it is the anatomical entity or the quality. For example, to prevent ontology "bloat", regions, margins, and projections of a bone are not in the anatomy ontology, but the bone itself is, and the concepts of margin, relative location of the margin (anterior, posterior, ventral, dorsal, etc), or bony projection are too, or are in other ontologies (spatial aspect, for example). Similarly, the directionality of a phenotype (such as a rotation, or curvature) isn't necessarily present in PATO, but the component terms necessary to express it are. The act of combining terms on-the-fly into cross-product terms is called post-composition, as opposed to pre-composed terms that are already in the ontology.

Post-composed terms can be created in Phenex following the genus-differentia principle of defining terms, where one term serves as the genus, which is then differentiated using a relationship and a differentia term. Unlike pre-composed terms, post-composed terms do not have an ID, and hence are "anonymous." Therefore if the same post-composition is used multiple times, it has the same semantics, but not the same identity. For example, if one wants to assign multiple annotations to the same process of the lateral ethmoid in the same specimen, using post-composed terms does not allow the identity of the anatomical structure between the annotations to be inferred.

The order in which the terms are composed is important if the composition relationship is not symmetric (a relationship is symmetric iff A rel B <=> B rel A). Most relationships are not symmetric. As a general rule, choose the more general part as the genus, and then use the relationship and differentia to narrow down. For example, for "process of the lateral ethmoid" use "process" as the genus, and use the relationship and differentia to narrow down which process of the many that are possible you mean, such as using part_of for the relationship and "lateral ethmoid" as the differentia (formally, the "process that is part_of the lateral ethmoid").

Note that semantically, the post-composed term is equivalent to a pre-composed term, provided the pre-composed term has both the inheritance relationship and the cross-product relationship properly recorded. For example, "process of lateral ethmoid" is-a "process", and "process of lateral ethmoid" part-of "lateral ethmoid".

Creating entity terms on-the-fly

To post-compose a term (for example, "maxillary process") using Phenex, first type in the genus term 'process' in the Entity field within the "Phenotypes" panel. Then open the Post-composition Editor box by right-clicking on the Entity cell (make sure that the entity cell is blue in color) :

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Now click on “Edit Post-composed Term.” The Editor box should now appear (see below), with “process” in the Genus field. The Genus is the feature of specific interest (varying feature in systematics). Click the “+” button to add a row in the table, type “part_of” in the relationship field, and type “maxilla” in the differentia field. Click OK.

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The post-composed term appears in the Entity field as:

process^part_of(maxilla)

Refining entities on-the-fly using spatial terms

Often we will want to include spatial information in a post-composed term. The Spatial Ontology is used to post-compose terms related to bone margins, surfaces, or regions. For example, the entity “anterior process of the maxilla" is post-composed as follows:

Within the Entity field, type “process” and right-click the field to open the Post-Composition Editor box. Within this box, Click the + button to add relationship = "part_of" and differentia = "anterior region". Right click on the differentia field to open another Post-Composition Editor box to add second post-composed term for "anterior margin of maxilla" (see below). Click the OK button after you have filled out the genus and differentia for this nested composition.

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Within Phenex, the post-composed term for process on the anterior margin of the maxilla appears as:

process^part_of(anterior region^part_of(maxilla))

As for semantics, identifiability, and rules for post-composing, the same applies as above for entity terms applies to spatial terms. In creating the nested term "anterior region of maxilla", start with the more general term (for example, the "anterior region") as the genus, then refine it using a relationship and a differentia term (for example, anterior region that is part_of the "supraorbital bone").

Creating "joint" terms on-the-fly

Joints are defined in TAO according to the bones that participate in the joint. Because only regions of these bones are part_of the joint rather than the entire bone, we use the overlaps relation to define joints. For example, the frontal-pterotic joint has the following relationships:

Definition:
Joint that articulates the frontal and pterotic. Frontal-pterotic joint is paired.

relationships:
is_a joint

frontal overlaps frontal-pterotic joint
pterotic overlaps frontal-pterotic joint

If it is unlikely that a joint term will be used repeatedly for annotation, then a term for the joint can be post-composed using Phenex. To post-compose metapterygoid-hyomandibular joint, for example, open the post-composition editor box by right-clicking on the Entity field, and enter the following terms in the window:

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The post-composed term for metapterygoid-hyomandibular joint will appear as:

joint^overlaps(metapterygoid)^overlaps(hyomandibula)

Evidence Codes

**Note: Does not apply to current curation

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.

• Note: if there is a matrix in the paper, the IVS evidence code is assigned to all annotations linked to the character list.

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.

How to write definitions for ontology terms

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 (described below) are terms created on-the-fly at the time of annotation, and take the form of genus-differentia definitions.