Refactor Sequence hierarchy to close #60

[allysonlister]

Note 1: clinical data item shows up in the diff below, though I didn't change it. This has come from an update of the external reference ontology, and has been updated in DRAO via Ontofox.

Note 2: the IAO annotation property alternative term has various labels, some of which are in other languages (see image below). It seems that the Robot diff has picked up one of these other language labels to use instead of the English alternative term, but please note that there is no error in the way the OWL file is written.

I have updated the development/refactored-IRIs-current.txt file with the following additions:

# List of refactored IRIs that have remained in DRAO.

Old IRI|New IRI
http://edamontology.org/data_2044|http://purl.obolibrary.org/obo/SO_0000001|Note: we are changing Sequence from EDAM to SO
http://edamontology.org/data_2976|http://purl.obolibrary.org/obo/SO_0000839|Note: we are changing Amino acid sequence from EDAM to SO

The following changes have been made, as compared by Robot diff on the master and branch version of DRAO-merged.owl:

Ontology comparison

Old

• Ontology IRI: http://www.fairsharing.org/ontology/domain/DRAO.owl
• Version IRI: None
• Loaded from: file:/home/.../domain-ontology/development/build/DRAO-merged.owl

New

• Ontology IRI: http://www.fairsharing.org/ontology/domain/DRAO.owl
• Version IRI: None
• Loaded from: file:/.../DRAO-merged-new.owl

Ontology imports

Ontology annotations

Nucleic acid sequence http://edamontology.org/data_2977

Removed

• Nucleic acid sequence SubClassOf Sequence

Added

• Nucleic acid sequence SubClassOf polypeptide_region

Protein sequence http://edamontology.org/data_2976

Removed

• Protein sequence label "Protein sequence"

• Protein sequence FAIRsharing alternative term "Amino acid sequence"@en

• Protein sequence inSubset "FAIRsharing"@en

• Protein sequence definition "One or more protein sequences, possibly with associated annotation."

• Protein sequence imported from EDAM.owl

• Protein sequence 替代术语 "Protein sequences"

• Class: Protein sequence

• Protein sequence SubClassOf Sequence

Sequence http://edamontology.org/data_2044

Removed

• Sequence imported from EDAM.owl

• Sequence label "Sequence"

• Sequence inSubset "FAIRsharing"@en

• Sequence 替代术语 "Sequences"

• Sequence definition "One or more molecular sequences, possibly with associated annotation."

• Class: Sequence

• Sequence SubClassOf Data

clinical data item http://purl.obolibrary.org/obo/OGMS_0000123

Removed

• clinical data item definition "a data item that is about a patient and is the specified output of a health care process assay or diagnostic process"

Added

• clinical data item definition "A data item that is about a patient and is the specified output of a health care process assay or diagnostic process"

polypeptide_region http://purl.obolibrary.org/obo/SO_0000839

Added

• polypeptide_region inSubset "FAIRsharing"@en

• polypeptide_region FAIRsharing alternative term "Amino acid sequence"@en

• polypeptide_region 替代术语 "Protein sequence"@en

region http://purl.obolibrary.org/obo/SO_0000001

Removed

• region label "region"

Added

• region inSubset "FAIRsharing"@en

• region FAIRsharing alternative term "Sequence"@en