ontology-access-kit
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INCATools
Ontology Access Kit: A python library and command line application for working with ontologies
## Overview I wasn't sure which implementation to use for to load an Obograph, but `OboGraphImplementation` seemed aptly named for this, so I gave it a go. However I got...
There are a lot of string fields using field names to group them into entities which would likely be better as `TermInfo` types. e.g. ```yaml classes: PairwiseSimilarity: abstract: true description:...
## Overview I'm trying to use OAK to get an Obograph, but `ProntoImplementation` took me 467 seconds to load it, where the `bioontologies` package took 48 seconds. ## Example **ProntoImplementation**...
## Overview I know it's probably almost always the case that someone will have an internet connection when developing/using, but it would be much more reliable / better UX if...
Should be possible to do `runoak --version` and introspect this
Currently we use a mixture of rdflib and sparqlwrapper in all sparql implementations (recall we also use sparql for local rdf files as well). These provide extremely low-level interfaces and...
Followed on from #305 - spellchecking (e.g https://github.com/FlyBase/flybase-ontology-scripts/blob/master/misc/obo_spellchecker.py) - punctuation - correct casing (e.g. https://github.com/cmungall/capital-offence) From @gouttegd > at FlyBase we have a small pronto-based script to do some minimal...
Interface: tbd - add to BasicOntologyInterface - make a new interface ? the input will be a curie or curies, and an optional list of preferred systems, drawn from: -...
The following paper https://philpapers.org/archive/SEPGFW.pdf lays out guidelines for definitions in ontologies I summarized these here: https://douroucouli.wordpress.com/2019/07/08/ontotip-write-simple-concise-clear-operational-textual-definitions/ Validation of a lot of these could be semi-automated; e.g. - S1: conform to...
https://ontobee.org/annotate/ consider a general ontoanimals implementation (we only have core ontobee so far)