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Ontologies Style Guide
AIM: This document aims to provide style guidance for names, definitions and comments in FlyBase ontologies. For more extensive style guidance, please refer to the GO curator guide.
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Aim to be reasonably descriptive, even at the risk of some verbal redundancy
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Where there are differences in the accepted spelling between English and US usage, use the US form, e.g. polymerizing, signaling, rather than polymerising, signalling.
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The aim of the ontology is to provide useable descriptions and links to the reader. Consequently, try to avoid obscure jargon (e.g. 'mereological') or pretentious latin/greek (e.g. genitalic), especially where widely understood, plain alternatives exist. Where it will aid searching, such terms may be added to synonyms and/or as asides within definitions. For example, 'lanceolate spermatid' is a descriptive term used in the literature. However, it is more commonly and plainly referred to as the 'leaf blade stage spermatid'. The plain use should be preferred with lanceolate only used in an aside: 'leaf blade (lanceolate) stage spermatid'.
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Yes to those that help clarity: Posterior-most (ie positional); Ventro-anterior (ie positional - see notes below); Where it is a regularly used/accepted hyphen in the literature (e.g.??). Pronoun or numeral (e.g. 'pro-England' or 'mid-60s').
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No to: Bona-fide; Prefix (sub, mid, semi, etc), unless it helps with clarity (e.g. multi-innervated). Hemi-desmosomes should be Hemidesmosomes. Posterior commissure (not posterior-commissure). (See notes below for multiple positional descriptors).
Consistency is important with marginal cases (e.g., always use multi-innervated throughout ontology; don't occasionally swap for multiinnervated).
Posteroanterior - this is the style used in Henderson's dictionary. Note also that we are used to seeing 'Ventrolateral' rather than 'ventrallateral'.
However, use a hyphen on more than two compounds, e.g. 'Ventroposterolateral' would be 'ventro-posterolateral'. There appears to be no real rule for this, so we seem to be free to adopt whichever we choose. I think hyphenating just two (e.g. ventro-lateral) conflicts with the literature too much (e.g. ventrolateral neurons rather than ventro-lateral), but not hyphenating compounds of 3 or more terms is too difficult to read.
These are so interchanged that they aren't really a rule anymore. However, as a guideline, use 'which' after a comma, and 'that' when no comma is used. e.g "This study, which cost $10,000, was a success." versus "The study that cost $10,000 was a success.".
Avoid abbreviations/contractions/symbols born out of laziness to type (such as '&' or '+' (meaning 'and'); or 'Vs' for versus; or using the short synonym of a term). Abbreviations or shorter synonyms are acceptable when they are commonly understood or they really do help to reduce the amount of typing enough to help readability.
According to GO, "Avoid abbreviations unless they're self-explanatory. Use full element names, not symbols. Use hydrogen for H+. Use copper and zinc rather than Cu and Zn. Use copper(II), copper(III), etc., rather than cuprous, cupric, etc.. For biomolecules, spell out the term in full wherever practical: use fibroblast growth factor, not FGF."
Use the singular form for the name, and begin the definition as a definition of this singular form. Expansion of the definition can then enter into plural if needed. For example:
id: FBbt:00001587 name: IP neuron def: "Serotonergic neuron whose cell body is located in one of 2 (bilateral) clusters in the brain (note: explains what a singular IP neuron is...): in the larva these clusters (...and then disucsses that they are found in clusters, and converts to plural) occupy the ventral cortex (rind) adjacent to the esophagus aperture; in the adult they are located in the cortex of the inferior-medial protocerebrum." [FlyBase:FBrf0048551]
All lower case except where demanded by context, e.g. DNA, not dna.
- Traditionally, we have used: 'maybe Bolwig's nerve?'
- Rewrite this as "Possible equivalence with ...". Where possible, a reference for why we have this assertion should be provided. Do not use a question mark. Using a search for 'Possible' allows us to find these terms in the future.
OBO format unfortunately has no internal notes field, so we have traditionally added these to the OBO comment field, which we also use for publicly visible comments. Suggested standardisation for these: "Ontology note: ... -[FBC:david]".
Preferably not. The definition should have the sense of being definitive, which is undermined if we show doubt. Any doubts should be added to the comments which should include a reason for this doubt and/or a reference (personal communications are acceptable for this where no other references exist).
This is a stub - a place holder for future documentation.
For the ontology, the larval stages will be classsified as a continuation of the embryo. Thus, if a structure develops in the embryo and is known to be found in the larva, it will be referred to as embryonic/larval.
If a term is used in the definition which differs from the used name (e.g. globuli cell bodies' for 'kenyon cells') this must be included as a synonym for the original term.