getCellOnto: basic getters in old style, retained 2023 for deprecation...

In vjcitn/ontoProc: processing of ontologies of anatomy, cell lines, and so on

basic getters in old style, retained 2023 for deprecation interval

Description

basic getters in old style, retained 2023 for deprecation interval

Usage

getChebiLite()

getCellosaurusOnto()

getUBERON_NE()

getChebiOnto()

getOncotreeOnto()

getDiseaseOnto()

getGeneOnto()

getHCAOnto()

getPROnto()

getPATOnto()

getMondoOnto()

getSIOOnto()

Value

instance of ontology_index (S3) from ontologyIndex

Note

getChebiOnto loads ontoRda/chebi_full.rda

getOncotreeOnto loads ontoRda/oncotree.rda

getDiseaseOnto loads ontoRda/diseaseOnto.rda

getHCAOnto loads ontoRda/hcaOnto.rda produced from hcao.owl at https://github.com/HumanCellAtlas/ontology/releases/tag/1.0.6 2/11/2019, python pronto was used to convert OWL to OBO.

getPROnto loads ontoRda/PRonto.rda, produced from http://purl.obolibrary.org/obo/pr.obo 'reasoned' ontology from OBO foundry, 02-08-2019. In contrast to other ontologies, this is imported via get_OBO with ‘extract_tags=’minimal''.

getPATOnto loads ontoRda/patoOnto.rda, produced from https://raw.githubusercontent.com/pato-ontology/pato/master/pato.obo from OBO foundry, 02-08-2019.

vjcitn/ontoProc documentation built on March 23, 2024, 7:23 a.m.