v2022-05-23

What's Changed

• change label 'utilizes' to 'device utilizes material' by @wdduncan in #605
• fixed superclasses fixes #369 by @pgaudet in #608
• Adding "surface of" alt label by @ddooley in #604

New Contributors

• @ddooley made their first contribution in #604

Full Changelog: v2022-04-25...v2022-05-23

2022-04-25 Release

What's Changed

• Remove Shorthand annotations, fixes issues stated in #601
• Fix datetime format for recently added term. by @balhoff in #572
• Adding "has exposure medium" relation by @laurenechan in #534
• added plasma membrane relations by @shawntanzk in #578
• Some clarification on reflexivity by @cmungall in #570
• Adding RO templates, including for interaction patterns. Addresses #521 by @cmungall in #581
• Make overlaps symmetric by @matentzn in #584
• myristoylates. Fixes #521 by @cmungall in #586
• pattern pipeline tweak by @cmungall in #588
• Bridge BFO role to CHEBI role. by @balhoff in #528
• Clean up ro-metamodel.yaml by @cthoyt in #590
• Add additional PTMs by @cthoyt in #589
• DO NOT MERGE: new template based editing pipeline by @matentzn in #466
• template docs by @cmungall in #592
• Submission of ADO and EPIO related relations by @BideZ in #593

New Contributors

• @BideZ made their first contribution in #593

Full Changelog: v2022-02-07...v2022-04-25

2022-02-07 Release

What's Changed

• Ensure that targets needed for release are dependencies for release. by @balhoff in #560
• Removes some broken links by @matentzn in #559
• Moving PATO OP to RO by @shawntanzk in #567
• Added properties for marker set by @shawntanzk in #545

Full Changelog: v2022-01-20...v2022-02-07

2022-01-20 release

This release is primarily to properly update the subsets for the previous release.

What's Changed

• Added info about mailing list and meetings by @nlharris in #557
• added "How to contribute to RO and join the RO working group" by @nlharris in #558

Full Changelog: v2022-01-19...v2022-01-20

2022-01-19 release

What's Changed

• Add ID range for Charlie Hoyt by @cthoyt in #538
• Fix dc:license by @shawntanzk in #539
• Adds domain and range reasoning to ro.owl by @matentzn in #520
• Add "has driver" and "has disease driver" to RO by @lschriml in #531
• Add ID range for Jim Balhoff by @balhoff in #542
• Fixes for branching structures by @cmungall in #537
• fix IRI for utilizes by @wdduncan in #548
• Fix expansion of never_in_taxon to use correct syntax. by @gouttegd in #549
• Add 'regulates characteristic' relations. by @balhoff in #543
• gene to disease relations reclassification and new term by @sabrinatoro in #553
• Remove deprecated inverse assertion by @matentzn in #554
• Add property chains to regulation of characteristics. by @balhoff in #555

New Contributors

• @cthoyt made their first contribution in #538
• @gouttegd made their first contribution in #549

Full Changelog: v2021-12-07...v2022-01-19

2021-12-07 release

What's Changed

• google analytics by @cmungall in #512
• process docs by @cmungall in #513
• Issue 497: add utilizes relation by @wdduncan in #511
• fix misspelling in 'occurrent part of' by @nicolevasilevsky in #517
• Update process-relations.md by @nicolevasilevsky in #519
• Add has phenotype or disease and has disease by @laurenechan in #507
• updated label name to 'disease arises from alteration in structure' by @sabrinatoro in #510
• Update ro-idranges.owl by @lschriml in #529
• Fixes geneontology/go-ontology#22488 by @cmungall in #532

New Contributors

• @laurenechan made their first contribution in #507
• @lschriml made their first contribution in #529

Full Changelog: v2021-10-27...v2021-12-07

2021-10-27 Release

Terms Added:
has exemplar data
exemplar data of
subcluster of

Edits:
Changed 'hyperparasitoid of" to be a narrow synonym (see #501)

Release 2021-08-31

• new relation "has component participant"
• new SWRL rule over RO:0002411

See git diff

release 2021-08-25

no changes

2021-08-04 release

Changes:

Left

• Ontology IRI: http://purl.obolibrary.org/obo/ro.owl
• Version IRI: http://purl.obolibrary.org/obo/ro/releases/2021-06-23/ro.owl

Right

• Ontology IRI: http://purl.obolibrary.org/obo/ro.owl
• Version IRI: http://purl.obolibrary.org/obo/ro/releases/2021-08-04/ro.owl

GO_0044403 http://purl.obolibrary.org/obo/GO_0044403

Removed

• GO_0044403 SubClassOf is symbiosis some Self

GO_0072519 http://purl.obolibrary.org/obo/GO_0072519

Removed

• GO_0072519 SubClassOf is parasitism some Self

GO_0085030 http://purl.obolibrary.org/obo/GO_0085030

Removed

• GO_0085030 SubClassOf is mutualism some Self

GO_0085031 http://purl.obolibrary.org/obo/GO_0085031

Removed

• GO_0085031 SubClassOf is commensalism some Self

Rules

Removed

• enables(?x, ?y), occurs in(?y, ?z) -> part of(?x, ?z)
  • comment "This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps""

commensually interacts with http://purl.obolibrary.org/obo/RO_0002441

Removed

• commensually interacts with is symmetric relational form of process class GO_0085031

disease arises from structure http://purl.obolibrary.org/obo/RO_0004030

Removed

• disease arises from structure definition "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure."

Added

• disease arises from structure definition "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles."

has phenotype http://purl.obolibrary.org/obo/RO_0002200

Removed

• has phenotype SubPropertyOf: topObjectProperty

has synaptic IO in http://purl.obolibrary.org/obo/RO_0013001

Removed

• has synaptic IO in label "has synaptic IO in"@en

Added

• has synaptic IO in label "has synaptic IO in region"@en

innervates http://purl.obolibrary.org/obo/RO_0002134

Removed

• innervates SubPropertyOf: topObjectProperty

interacts with via parasite-host interaction http://purl.obolibrary.org/obo/RO_0002443

Removed

• interacts with via parasite-host interaction is symmetric relational form of process class GO_0072519

mutualistically interacts with http://purl.obolibrary.org/obo/RO_0002442

Removed

• mutualistically interacts with is symmetric relational form of process class GO_0085030

obsolete actively participates in http://purl.obolibrary.org/obo/RO_0002217

Removed

• obsolete actively participates in label "obsolete actively participates in"@en

Added

• obsolete actively participates in label "obsolete actively participates in"^^string
• obsolete actively participates in term replaced by process has causal agent

obsolete has active participant http://purl.obolibrary.org/obo/RO_0002218

Removed

• obsolete has active participant in_subset eco subset

• obsolete has active participant definition "x has participant y if and only if x realizes some active role that inheres in y"

• obsolete has active participant has curation status pending final vetting

• obsolete has active participant editor note "This may be obsoleted and replaced by the original 'has agent' relation"

• obsolete has active participant example of usage "'heart development' has active participant some Shh protein"

Added

• obsolete has active participant definition "OBSOLETE x has participant y if and only if x realizes some active role that inheres in y"

• obsolete has active participant term replaced by causal agent in process

parasite of http://purl.obolibrary.org/obo/RO_0002444

Removed

• parasite of is asymmetric relational form of process class GO_0072519

phenotype of http://purl.obolibrary.org/obo/RO_0002201

Removed

• phenotype of SubPropertyOf: topObjectProperty

receives synaptic input from neuron http://purl.obolibrary.org/obo/RO_0013008

Added

• receives synaptic input from neuron label "receives synaptic input from neuron"@en

• receives synaptic input from neuron definition "A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it."

• receives synaptic input from neuron creation_date "2021-05-26T08:40:18Z"^^dateTime

• receives synaptic input from neuron created_by 0000-0002-1373-1705

• ObjectProperty: receives synaptic input from neuron

• receives synaptic input from neuron InverseOf sends synaptic output to cell

• receives synaptic input from neuron SubPropertyOf: synapsed by

receives synaptic input in http://purl.obolibrary.org/obo/RO_0013002

Removed

• receives synaptic input in label "receives synaptic input in"@en

Added

• receives synaptic input in label "receives synaptic input in region"@en

releases neurotransmitter http://purl.obolibrary.org/obo/RO_0002111

Removed

• releases neurotransmitter SubPropertyOf: topObjectProperty

sends synaptic output to http://purl.obolibrary.org/obo/RO_0013003

Removed

• sends synaptic output to label "sends synaptic output to"@en

Added

• sends synaptic output to label "sends synaptic output to region"@en ...