Curator guidelines

DRAFT (just to take notes at this point)

format

• A line in the file represents an information of similarity; it does not capture the ancestral taxon.

NOT annotations

Different use cases of NOT annotations:

• contradicting a homology hypothesis (provide example)
• cases of independent evolution (provide example)

In case of NOT annotations for independent evolution: always try to capture all taxa where the structure independently evolved (see issue #5)

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Example case of independent evolution:

"Amphibians have a three-chambered heart, whereas mammalian, crocodilian and avian hearts have four chambers, two each for pulmonary and systemic circulations. The acquisition of a fully septated ventricle has evolved independently in birds, mammals and crocodilians, and is an important example of convergent evolution."

Annotation for interventricular septum (UBERON:0002094):

• • NOT amniota
• • positive annotation on Mammalia
• • positive annotation on Aves
• • positive annotation on Crocodylia

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Multiple-entities annotation

When more than a structure is annotated for homology,

for example

UBERON:1500000|UBERON:0007174 scapular blade|medial border of scapula

for homology on 32524 Amniota

we annotate also each single entity (usually by ECO:0000355 phylogenetic distribution evidence)

UBERON:1500000 scapular blade --> Aves

UBERON:0007174 medial border of scapula --> Mammalia

BUT if the single-entity has the same taxon level than the multiple-entities annotation, we do not provide single-entity annotation (ex. lung|swim bladder on Gnathostomata, no single annotation on lung, as the primitive lung is from Gnathostomata too)

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Choose the correct class

(adapted from C.Mungall, see https://github.com/BgeeDB/anatomical-similarity-annotations/issues/9)

It is sometimes difficult to choose the correct class to report an annotation when we have a loose concept represented by multiple more formally defined classes. For example, if the osculum is homologous to the mouth, what is the mouth exactly?

which of these?

UBERON:0000165 ! mouth
UBERON:0000166 ! oral opening
UBERON:0000167 ! oral cavity

We can postulate that for gene expression curation we never want to choose a space. Genes are always initially expressed in a cell, which may be located in a space, but not part of it. We can then just ditch all subclasses for space for all our curation.