merge changes for 2.13 #116
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Removing cases where a birnlex_ fragment was move from one namespace
to another to simplify namespace issues. Removed:
BIRNOBO:birnlex_1 -> NIFMOL
BIRNOBO:birnlex_2 -> NIFORG
BIRNOBO:birnlex_3 -> NIFGA
BIRNOBO:birnlex_10 -> NIFSUB
BIRNOBO:birnlex_11 -> NIFGA
BIRNOBO:birnlex_13 -> NIFSUB
BIRNOBO:birnlex_15 -> NIFMOL
BIRNOBO:birnlex_21 -> NIFMOL
BIRNOBO:birnlex_22 -> NIFMOL
…o now deleted duplicate fragment identifiers
Turns out that the issues with hasTaxonRank were the result of an 'off by 6310' error, and a reminder why using annotation properties to hold identifiers isn't alwasy the best idea. Not entirely sure how the issue came about (some script running a regex that hit stuff out of scope?) but it has been there for years. Now resolved.
…ult namespace between BIRNOBI and NIFINV
At some point in the past a default namespace copying error occured which injected birnlex_2107 into the NIFQUAL namespace instead of leaving it in the NIFINV namespace. This commit merges NIFQUAL:2107 back into NIFINV:2107, removing the NIFQUAL version of the identifier.
…se it was originally used only fire NIFQUAL retired classes, all of which haven't actually been marked as deprecated...
…re, I suspect this was missed in an earlier cleanup
…converting back for consistency
sao225178797 survived retirement and still has a version in the NIFMOL namespace added NIFMOL NIFSUB prefixes
This commit fixes the fact that NIFNEURON:nlx_cell_10061313 is calretinin neuron, while NIFNEURBR2:nlx_cell_10061313 is cerebellar nucleus neuroa. Given the context of the NIFNEURBR2 version I am going to interpret it as a typo since NIFNEURBR2:nlx_cell_10061414 is cerebellar cortex neuron. Thus my correctino is the following. Convert NIFNEURBR2:nlx_cell_10061313 -> NIFNEURBR2:nlx_cell_10061413. This is also a better solution since NIFNEURON:nlx_cell_10061313 has been used far more widely including in the HBP cell ontology.
Over time various kinds of copy paste errors have led to annotation properties defined in OBOANN and BIRNANN to be placed in the wrong namespace. This commit corrects those issues and also removes a couple of deprecated classes. All files modified were also reserialized so that their ordering is correct.
…edID back in 2008 >_<
These changes are the product of running parcellation.py at commit e45e010bba76a0cb41a54f2516725ef443e63b24. Base IRIs have been reworked to experiment with using interlex namespaces to provide globally resolvable identifiers in cases where the source only provides local identifiers.
…es as a sentinel to prevent use of the empty namespace
The old identifier was http://www.owl-ontologies.com/Ontology1272057115.owl#nlx_cell_1006007 now NIFCELL:nlx_cell_1006007 Not doing the normal deprecation practice due to common fragment issues.
Removed <http://www.owl-ontologies.com/Ontology1272057115.owl#CHEBI_46643> class since there are no references it that iri and CHEBI:46643 now has all the relevant information that we had collected about it.
…resent in taxslim or as synonyms in NIFORG
We now import go.owl via go-bridge.ttl. This replaces the old GO-CC-Bridge, leaving out SOA equivalence axioms that caused fundamental reasoning errors while preserving the positioning of the GO roots in BFO.
We now import taxslim.owl and NIF-Organism.ttl via tax-bridge.ttl. There are a number of axioms that are currently in the Eagle-I bridge that can be ported over, in the time before we move to deprecate parts of NIFORG.
UBERON:0000465 is a material anatomical entity, the old modelling which I copied places it under IndependentContinuant, but it make make more sense under MaterialEntity (or as a multi parent).
…na is part of the peripheral nervous sytem, this bug is still present on the NIFGA ids (wontfix)
…that this is not simply a clone of the purl.obolibrary.org version
This is a hefty commit that makes some fundamental changes to reconcile the anatomical modellingin NIFGA and UBERON. The major changes are 1. Removal of has_proper_part and proper_part_of axioms that asserted that parts of the peripheral nervous sytem were part of the central nervous system. These were removed in both nifga proper and uberon-bridge where they had perviously been ported. 2. Removal of disjointness axioms between Regional part of X and X that conflict with uberon's modelling where a part of X can also be sco X. 3. Relaxation of sco hierarchy (usually in the regional part of x which has been deprecated in uberon) to avoid part of pns vs part of cns disjointness in uberon (related to 1). Two additional changes have been made. 1. The local copy of uberon.owl has been patched to reflect the changes discussed in obophenotype/uberon#1356. 2. The label of BIRNLEX:2529 was updated to correct an ancient copy and paste error so that it now properly matchs UMLS:C1184863. @cmungall See obophenotype/uberon#1357 for refernce. This is part 1 of the changes. The additional changes are a bit deeper and either require changes to uberon-bridge-to-nifstd or something much deeper due to conflicts between acellular and multicellular parts.
Switched subClassOf Regional Part of to proper_part_of for membranes which were subclassed to things that are now organs. This mirrors the modelling in uberon for skirting issues with acellular vs multicellular anatomical structures. Some addional changes in uberon-bridge are not real changes but reordering because I previously forgot to run ttlfmt on the file. See aslo obophenotype/uberon#1358
…F* iri release, included NIFGA in import chain in anatomy-bridge
…er.patch to reflect changes
This is the final commit where the ontology will use the old ontology.neuinfo.org iris for entities. 'Bumping' (down) to 2.13 for the release. The reasoner actually runs on everything and most of the import chain has been reworked. Many more changes incoming in prep for 3.0.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
First round of changes needed prior to executing the uri switch and backend refactor needed for a full 3.0 release. This includes, major changes to the import chain and culling of unused/unneeded classes, annotation properties, object properties, and axioms. It also includes a 'loosening' of the NIFGA modelling so that it will be minimally compatible with Uberon so that the full transition to Uberon can be made more seamlessly.
Misc