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Ontology Access Kit: A python library and command line application for working with ontologies

Home Page: https://incatools.github.io/ontology-access-kit/

License: Apache License 2.0

Makefile 0.05% Jupyter Notebook 72.55% Python 27.34% HTML 0.06%

apis geneontology monarchinitiative oaklib obofoundry ontology ontology-api owl python rdf semantic-web

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Add a notebook demonstrating mappings

in the notebooks/ folder

rough script of ow it should work:

part 1 - fetching existing mappings

extract a sssom file from bioportal
extract a sssom file from a downloaded ontology

choose an uberon. term like limb as an example

part 2 - generating mappings

choose two small ontologies, e.g. zfa and xao, demonstrate using lexmatch to find mappings

Add a generate-categories method

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:

biolink
cob
UMLS STY
owl vocabulary (e.g. owl:Class)
design pattern

these are typically indicated via rdf:type (but not in OWL-DL), dc:conformsTo, subproperties of rdf:type (e.g. biolink:category)

the results will be an iterator of tuples (curie, system, category_curie)

Implementation:

not all implementations will be able to resolve this for all systems. if the preferred systems is empty, it will do a best effort. if preferred systems are passed and cannot be satisfied, throw a NotImplemented

for now start with ubergraph, this precomputes biolink categories, so it should be a simple lookup query

out of scope for this issue but in future:

add cob categories to ubergraph implementation, depends on INCATools/ubergraph#55
use either graph walking or relation-graph (e.g. for sqldb which already loads RG) to compute other categories - related to what @jhc is doing

On fetching ancestors — is this stated or reasoned? Does the query invoke the reasoner or are we assuming pre-classified?

From @hsolbrig

review cross-ontology-diff datamodel prior to implementing

Currently the cross-ontology-diff code uses an ad-hoc tuple as the output:

ontology-access-kit/src/oaklib/omk/omk_mapping_utils.py

Line 14 in 52771fe

 ANALOGOUS_RELATION = Tuple[DIFF_CATEGORY, CURIE, PRED_CURIE, CURIE, List[CURIE]] 

current results look like this:

('IDENTICAL', 'EMAPA:16037', 'rdfs:subClassOf', 'EMAPA:36032', [])
('OTHER', 'EMAPA:16041', 'rdfs:subClassOf', 'EMAPA:16039', [])

which is not so useful for review. We want to see labels, plus mapped concepts

We would like to move to a documented datamodel that may have applications beyond this software library:

https://incatools.github.io/ontology-access-kit/datamodels/cross-ontology-diff/index.html

Review this prior to implementing

Add to documentation: other ontology tools in py-land

Other libraries mentioned during the workshop we should add to the docs (either by adding the interfaces here, or by explaining why we don't)

set_label_for_curie not implemented for owl files?

The use case here is adding rdf labels to existing owl files using lexmatch from OAK. When you do this there is an error that the set_label_for_curie method is not implemented. Per @cmungall lexmatch rdflabel generation should work with the PRONTO implementation currently.

runoak -i ../../DLO/deep-learning-ontology/deep-learning-ontology-full.owl -a ../../DLO/deep-learning-ontology/external/ml-ontology-202010021305.owl lexmatch --add-labels
WARNING:root:Using rdflib rdf/xml parser; this behavior may change in future
WARNING:root:Using rdflib rdf/xml parser; this behavior may change in future
WARNING:root:Not a curie: deep-learning-ontology/deep-learning-ontology-full.owl
WARNING:root:Not a curie: deep-learning-ontology/deep-learning-ontology-full.owl
Traceback (most recent call last):
File "/Users/marcin/Documents/VIMSS/ontology/OAK/ontology-access-kit/venv/bin/runoak", line 8, in
sys.exit(main())
File "/Users/marcin/Documents/VIMSS/ontology/OAK/ontology-access-kit/venv/lib/python3.9/site-packages/click/core.py", line 1130, in call
return self.main(*args, **kwargs)
File "/Users/marcin/Documents/VIMSS/ontology/OAK/ontology-access-kit/venv/lib/python3.9/site-packages/click/core.py", line 1055, in main
rv = self.invoke(ctx)
File "/Users/marcin/Documents/VIMSS/ontology/OAK/ontology-access-kit/venv/lib/python3.9/site-packages/click/core.py", line 1657, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/Users/marcin/Documents/VIMSS/ontology/OAK/ontology-access-kit/venv/lib/python3.9/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/Users/marcin/Documents/VIMSS/ontology/OAK/ontology-access-kit/venv/lib/python3.9/site-packages/click/core.py", line 760, in invoke
return __callback(*args, **kwargs)
File "/Users/marcin/Documents/VIMSS/ontology/OAK/ontology-access-kit/venv/lib/python3.9/site-packages/oaklib/cli.py", line 1150, in lexmatch
add_labels_from_uris(impl)
File "/Users/marcin/Documents/VIMSS/ontology/OAK/ontology-access-kit/venv/lib/python3.9/site-packages/oaklib/utilities/lexical/lexical_indexer.py", line 46, in add_labels_from_uris
oi.set_label_for_curie(curie, label)
File "/Users/marcin/Documents/VIMSS/ontology/OAK/ontology-access-kit/venv/lib/python3.9/site-packages/oaklib/interfaces/basic_ontology_interface.py", line 203, in set_label_for_curie
raise NotImplementedError
NotImplementedError

High-level interface via the Bioregistry

The bioontologies package has a very high-level interface for getting OBO graphs by prefix, since it can automatically look up the appropriate IRIs via its mappings to OBO Foundry.

import bioontologies

parse_results = bioontologies.get_obograph_by_prefix("go")
go_graph_document = parse_results.graph_document

This could be extended to OAK and also let you choose if you want the OWL, OBO, or OBO Graph JSON artifact to get consumed

add version introspection

Should be possible to do runoak --version and introspect this

is there documentation on the search stuff (eg t~ etc.)?

reported by @shawntanzk

Missing images in Tutorial: Wing Vein

https://incatools.github.io/ontology-access-kit/intro/tutorial01.html

I see a missing image in the tutorial, linking to https://incatools.github.io/ontology-access-kit/intro/intro/wing-vein.png

I can see so far no images in the tutorial:

Where can I find this wing-vein.png
Where do you want images to be stored:
- Same dir as rst/md file
- docs/images

`poetry install` issue: ` • Installing scipy (1.6.1): Failed`

Description

I'm trying to use oaklib with mondo-analysis, but am having difficulty installing it.

I don't think it's available on pip yet.

I made a new pyproject.toml:

[tool.poetry]
name = "xxx"
version = "0.0.0"
description = "xxx"
authors = ["xxx"]

readme = "README.md"

[tool.poetry.dependencies]
python = "^3.9"
oaklib = ">0.0.0"

[tool.poetry.dev-dependencies]
pytest = "^5.2"

[build-system]
requires = ["poetry-core>=1.0.0"]
build-backend = "poetry.core.masonry.api"

[tool.poetry.scripts]
runoak = "oaklib.cli:main"
omk = "oaklib.omk.omk_cli:main"

[tool.poetry.extras]

I then ran:
python3 -m poetry install (I was having difficulty w/ normal poetry install; too many Python installations on my comp).

Error messages

python3 -m poetry install
Creating virtualenv xxx-iIwCVzCe-py3.9 in /Users/joeflack4/Library/Caches/pypoetry/virtualenvs
Updating dependencies
Resolving dependencies... (263.2s)

Writing lock file

Package operations: 116 installs, 0 updates, 0 removals

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  Invalid hashes (sha256:334a53f51b972b6df99ca2f5b723848472e5f130eed4189420ad85162f41d68e) for scipy (1.6.
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  Invalid hashes (sha256:334a53f51b972b6df99ca2f5b723848472e5f130eed4189420ad85162f41d68e) for scipy (1.6.
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  Invalid hashes (sha256:334a53f51b972b6df99ca2f5b723848472e5f130eed4189420ad85162f41d68e) for scipy (1.6.
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  RuntimeError

  Invalid hashes (sha256:334a53f51b972b6df99ca2f5b723848472e5f130eed4189420ad85162f41d68e) for scipy (1.6.
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  Invalid hashes (sha256:334a53f51b972b6df99ca2f5b723848472e5f130eed4189420ad85162f41d68e) for scipy (1.6.
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  RuntimeError

  Invalid hashes (sha256:334a53f51b972b6df99ca2f5b723848472e5f130eed4189420ad85162f41d68e) for scipy (1.6.
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  RuntimeError

  Invalid hashes (sha256:334a53f51b972b6df99ca2f5b723848472e5f130eed4189420ad85162f41d68e) for scipy (1.6.
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  RuntimeError

  Invalid hashes (sha256:334a53f51b972b6df99ca2f5b723848472e5f130eed4189420ad85162f41d68e) for scipy (1.6.
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  RuntimeError

  Invalid hashes (sha256:334a53f51b972b6df99ca2f5b723848472e5f130eed4189420ad85162f41d68e) for scipy (1.6.
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  RuntimeError

  Invalid hashes (sha256:334a53f51b972b6df99ca2f5b723848472e5f130eed4189420ad85162f41d68e) for scipy (1.6.
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  RuntimeError

  Invalid hashes (sha256:334a53f51b972b6df99ca2f5b723848472e5f130eed4189420ad85162f41d68e) for scipy (1.6.
  • Installing aiohttp (3.8.1)
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  • Installing fastobo (0.11.1)
  • Installing graphviz (0.20)
  • Installing joblib (1.1.0)
  • Installing linkml-dataops (0.1.0)
  • Installing more-click (0.1.1)
  • Installing myst-parser (0.17.2)
  • Installing networkx (2.8.1): Installing...
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  • Installing pyshex (0.8.1)
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  • Installing scipy (1.6.1): Failed

  RuntimeError

  Invalid hashes (sha256:334a53f51b972b6df99ca2f5b723848472e5f130eed4189420ad85162f41d68e) for scipy (1.6.
  • Installing parse (1.19.0): Installing...
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  • Installing pyshex (0.8.1)
  • Installing pystow (0.4.3)
  • Installing scipy (1.6.1): Failed

  RuntimeError

  Invalid hashes (sha256:334a53f51b972b6df99ca2f5b723848472e5f130eed4189420ad85162f41d68e) for scipy (1.6.
  • Installing pandas (1.4.2): Downloading... 90%
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  • Installing pyshex (0.8.1)
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  RuntimeError

  Invalid hashes (sha256:334a53f51b972b6df99ca2f5b723848472e5f130eed4189420ad85162f41d68e) for scipy (1.6.
  • Installing parse (1.19.0): Installing...
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  • Installing pyshex (0.8.1)
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  • Installing scipy (1.6.1): Failed

  RuntimeError

  Invalid hashes (sha256:334a53f51b972b6df99ca2f5b723848472e5f130eed4189420ad85162f41d68e) for scipy (1.6.
  • Installing pandas (1.4.2): Downloading... 100%
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  • Installing pyshex (0.8.1)
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  • Installing scipy (1.6.1): Failed

  RuntimeError

  Invalid hashes (sha256:334a53f51b972b6df99ca2f5b723848472e5f130eed4189420ad85162f41d68e) for scipy (1.6.
  • Installing parse (1.19.0): Installing...
  • Installing pydantic (1.9.0): Installing...
  • Installing pyshex (0.8.1)
  • Installing pystow (0.4.3)
  • Installing scipy (1.6.1): Failed

  RuntimeError

  Invalid hashes (sha256:334a53f51b972b6df99ca2f5b723848472e5f130eed4189420ad85162f41d68e) for scipy (1.6.
  • Installing pandas (1.4.2): Downloading... 100%
  • Installing parse (1.19.0): Installing...
  • Installing pydantic (1.9.0): Installing...
  • Installing pyshex (0.8.1)
  • Installing pystow (0.4.3)
  • Installing scipy (1.6.1): Failed

  RuntimeError

  Invalid hashes (sha256:334a53f51b972b6df99ca2f5b723848472e5f130eed4189420ad85162f41d68e) for scipy (1.6.
  • Installing pyshex (0.8.1)
  • Installing pystow (0.4.3)
  • Installing scipy (1.6.1): Failed

  RuntimeError

  Invalid hashes (sha256:334a53f51b972b6df99ca2f5b723848472e5f130eed4189420ad85162f41d68e) for scipy (1.6.
  • Installing pydantic (1.9.0)
  • Installing pyshex (0.8.1)
  • Installing pystow (0.4.3)
  • Installing scipy (1.6.1): Failed

  RuntimeError

  Invalid hashes (sha256:334a53f51b972b6df99ca2f5b723848472e5f130eed4189420ad85162f41d68e) for scipy (1.6.
  • Installing parse (1.19.0): Installing...
  • Installing pydantic (1.9.0)
  • Installing pyshex (0.8.1)
  • Installing pystow (0.4.3)
  • Installing scipy (1.6.1): Failed

  RuntimeError

  Invalid hashes (sha256:334a53f51b972b6df99ca2f5b723848472e5f130eed4189420ad85162f41d68e) for scipy (1.6.
  • Installing pandas (1.4.2): Installing...
  • Installing parse (1.19.0): Installing...
  • Installing pydantic (1.9.0)
  • Installing pyshex (0.8.1)
  • Installing pystow (0.4.3)
  • Installing scipy (1.6.1): Failed

  RuntimeError

  Invalid hashes (sha256:334a53f51b972b6df99ca2f5b723848472e5f130eed4189420ad85162f41d68e) for scipy (1.6.
  • Installing openpyxl (3.0.9)
  • Installing pandas (1.4.2): Installing...
  • Installing parse (1.19.0): Installing...
  • Installing pydantic (1.9.0)
  • Installing pyshex (0.8.1)
  • Installing pystow (0.4.3)
  • Installing scipy (1.6.1): Failed

  RuntimeError

  Invalid hashes (sha256:334a53f51b972b6df99ca2f5b723848472e5f130eed4189420ad85162f41d68e) for scipy (1.6.
  • Installing networkx (2.8.1)
  • Installing openpyxl (3.0.9)
  • Installing pandas (1.4.2): Installing...
  • Installing parse (1.19.0): Installing...
  • Installing pydantic (1.9.0)
  • Installing pyshex (0.8.1)
  • Installing pystow (0.4.3)
  • Installing scipy (1.6.1): Failed

  RuntimeError

  Invalid hashes (sha256:334a53f51b972b6df99ca2f5b723848472e5f130eed4189420ad85162f41d68e) for scipy (1.6.
  • Installing pydantic (1.9.0)
  • Installing pyshex (0.8.1)
  • Installing pystow (0.4.3)
  • Installing scipy (1.6.1): Failed

  RuntimeError

  Invalid hashes (sha256:334a53f51b972b6df99ca2f5b723848472e5f130eed4189420ad85162f41d68e) for scipy (1.6.
  • Installing parse (1.19.0)
  • Installing pydantic (1.9.0)
  • Installing pyshex (0.8.1)
  • Installing pystow (0.4.3)
  • Installing scipy (1.6.1): Failed

  RuntimeError

  Invalid hashes (sha256:334a53f51b972b6df99ca2f5b723848472e5f130eed4189420ad85162f41d68e) for scipy (1.6.
  • Installing parse (1.19.0)
  • Installing pydantic (1.9.0)
  • Installing pyshex (0.8.1)
  • Installing pystow (0.4.3)
  • Installing scipy (1.6.1): Failed

  RuntimeError

  Invalid hashes (sha256:334a53f51b972b6df99ca2f5b723848472e5f130eed4189420ad85162f41d68e) for scipy (1.6.
  • Installing pandas (1.4.2)
  • Installing parse (1.19.0)
  • Installing pydantic (1.9.0)
  • Installing pyshex (0.8.1)
  • Installing pystow (0.4.3)
  • Installing scipy (1.6.1): Failed

  RuntimeError

  Invalid hashes (sha256:334a53f51b972b6df99ca2f5b723848472e5f130eed4189420ad85162f41d68e) for scipy (1.6.1) using archive scipy-1.6.1-cp39-cp39-macosx_10_9_x86_64.whl. Expected one of sha256:0c8a51d33556bf70367452d4d601d1742c0e806cd0194785914daf19775f0e67, sha256:0e5b0ccf63155d90da576edd2768b66fb276446c371b73841e3503be1d63fb5d, sha256:2481efbb3740977e3c831edfd0bd9867be26387cacf24eb5e366a6a374d3d00d, sha256:33d6b7df40d197bdd3049d64e8e680227151673465e5d85723b3b8f6b15a6ced, sha256:5da5471aed911fe7e52b86bf9ea32fb55ae93e2f0fac66c32e58897cfb02fa07, sha256:5f331eeed0297232d2e6eea51b54e8278ed8bb10b099f69c44e2558c090d06bf, sha256:5fa9c6530b1661f1370bcd332a1e62ca7881785cc0f80c0d559b636567fab63c, sha256:6725e3fbb47da428794f243864f2297462e9ee448297c93ed1dcbc44335feb78, sha256:68cb4c424112cd4be886b4d979c5497fba190714085f46b8ae67a5e4416c32b4, sha256:794e768cc5f779736593046c9714e0f3a5940bc6dcc1dba885ad64cbfb28e9f0, sha256:83bf7c16245c15bc58ee76c5418e46ea1811edcc2e2b03041b804e46084ab627, sha256:8e403a337749ed40af60e537cc4d4c03febddcc56cd26e774c9b1b600a70d3e4, sha256:a15a1f3fc0abff33e792d6049161b7795909b40b97c6cc2934ed54384017ab76, sha256:a423533c55fec61456dedee7b6ee7dce0bb6bfa395424ea374d25afa262be261, sha256:a5193a098ae9f29af283dcf0041f762601faf2e595c0db1da929875b7570353f, sha256:bd50daf727f7c195e26f27467c85ce653d41df4358a25b32434a50d8870fc519, sha256:c4fceb864890b6168e79b0e714c585dbe2fd4222768ee90bc1aa0f8218691b11, sha256:e79570979ccdc3d165456dd62041d9556fb9733b86b4b6d818af7a0afc15f092, sha256:f46dd15335e8a320b0fb4685f58b7471702234cba8bb3442b69a3e1dc329c345.

  at ~/Library/Python/3.9/lib/python/site-packages/poetry/installation/executor.py:627 in _download_link
      623│                     )
      624│                 )
      625│
      626│             if archive_hashes.isdisjoint(hashes):
    → 627│                 raise RuntimeError(
      628│                     "Invalid hashes ({}) for {} using archive {}. Expected one of {}.".format(
      629│                         ", ".join(sorted(archive_hashes)),
      630│                         package,
      631│                         archive_path.name,

  • Installing sphinx-click (4.0.3)
  • Installing sphinx-rtd-theme (1.0.0)
  • Installing sqlalchemy (1.4.36)
  • Installing watchdog (2.1.8)

Search behavior on obo files not as expected

I noticed this first when going through the tutorials and running search via the cli:

runoak --input obolibrary:fbbt.obo search 'wing vein'

What is expected in the tutorial is:

FBbt:00004751 ! wing vein
FBbt:00004754 ! axillary vein
FBbt:00004759 ! wing vein L1
FBbt:00004760 ! wing vein L2

But what is returned by OAK is:

FBbt:00004751 ! wing vein

This behavior is seen on:

main (ref 9bd64d9)
v0.1.19

After a bit of tinkering I realized that this might be because the default search behavior might have changed from SearchTermSyntax.REGULAR_EXPRESSION to SearchTermSyntax.STARTS_WITH.

Add an owlery implementation

Use case: dynamic reasoning

Use https://github.com/phenoscape/python-owlery-client, see phenoscape/owlery#200

consider adding list of ontologies for annotate subcommand

from @turbomam

Avoid checking .md files into repo

We should have the sphinx docgen step preceded by make gendoc which uses linkml docgen to generate the md files

decide on method names

@matentzn should be identifier not curie
@matentzn "is it pythonic to not use get, add or is in front of method names like we do in Java land?"

Align metrics with robot measure?

I was looking at https://incatools.github.io/ontology-access-kit/datamodels/summary-statistics/index.html

I have created quite an extensive set of metrics for ontologies for
https://robot.obolibrary.org/measure

Maybe we should align these?

Change label to lbl in obograph datamodel

This will temporarily break things in, but it aligns with the actual obographjson standard

Ensure curies are always curies

many of the datamodels force the use of CURIEs

sometimes applying naive uri-to-curie yields things like

uberon/core#BRAIN:NAME:ABV

not clear if this is due to some kind of roundtrip through obo but either way the code should be robust and always yield CURIEs where these are expected

Searches on `cl.obo`, `uberon.obo` fail

I'm following the tutorial, and diverged a bit to try searches in other OBO ontologies.

The following search fails:

$ runoak -i obolibrary:cl.obo search 'epithelial cell of lung'
/home/harry/oak-tutorial/oak-env/lib/python3.9/site-packages/pronto/parsers/_fastobo.py:84: SyntaxWarning: source document contains incomplete creation date: 2021-11-08
  process_clause_typedef(clause, data, self.ont)
/home/harry/oak-tutorial/oak-env/lib/python3.9/site-packages/pronto/parsers/_fastobo.py:84: NotImplementedWarning: cannot process `equivalent_to_chain: attaches_to part_of` macro
  process_clause_typedef(clause, data, self.ont)
Traceback (most recent call last):
  File "/home/harry/oak-tutorial/oak-env/bin/runoak", line 8, in <module>
    sys.exit(main())
  File "/home/harry/oak-tutorial/oak-env/lib/python3.9/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/home/harry/oak-tutorial/oak-env/lib/python3.9/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/home/harry/oak-tutorial/oak-env/lib/python3.9/site-packages/click/core.py", line 1654, in invoke
    super().invoke(ctx)
  File "/home/harry/oak-tutorial/oak-env/lib/python3.9/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/harry/oak-tutorial/oak-env/lib/python3.9/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/home/harry/oak-tutorial/oak-env/lib/python3.9/site-packages/oaklib/cli.py", line 140, in main
    settings.impl = impl_class(resource)
  File "<string>", line 6, in __init__
  File "/home/harry/oak-tutorial/oak-env/lib/python3.9/site-packages/oaklib/implementations/pronto/pronto_implementation.py", line 73, in __post_init__
    ontology = Ontology.from_obo_library(resource.slug)
  File "/home/harry/oak-tutorial/oak-env/lib/python3.9/site-packages/pronto/ontology.py", line 206, in from_obo_library
    return cls(
  File "/home/harry/oak-tutorial/oak-env/lib/python3.9/site-packages/pronto/ontology.py", line 283, in __init__
    cls(self).parse_from(_handle)  # type: ignore
  File "/home/harry/oak-tutorial/oak-env/lib/python3.9/site-packages/pronto/parsers/obo.py", line 48, in parse_from
    self.symmetrize_lineage()
  File "/home/harry/oak-tutorial/oak-env/lib/python3.9/site-packages/pronto/parsers/base.py", line 84, in symmetrize_lineage
    graphdata.lineage[superentity].sub.add(subentity)
KeyError: 'CARO:0000000'

Looks like a pronto parsing issue?

Searching cl.owl instead produces numerous errors but eventually yields the desired result (CL:0000082 ! epithelial cell of lung)

I get a similar result when running

$ runoak -i obolibrary:uberon.obo search 'epithelial cell'

for Uberon, though in that case searching uberon.owl instead raises an AttributeError:

Traceback (most recent call last):
  File "/home/harry/oak-tutorial/oak-env/bin/runoak", line 8, in <module>
    sys.exit(main())
  File "/home/harry/oak-tutorial/oak-env/lib/python3.9/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/home/harry/oak-tutorial/oak-env/lib/python3.9/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/home/harry/oak-tutorial/oak-env/lib/python3.9/site-packages/click/core.py", line 1654, in invoke
    super().invoke(ctx)
  File "/home/harry/oak-tutorial/oak-env/lib/python3.9/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/harry/oak-tutorial/oak-env/lib/python3.9/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/home/harry/oak-tutorial/oak-env/lib/python3.9/site-packages/oaklib/cli.py", line 140, in main
    settings.impl = impl_class(resource)
  File "<string>", line 6, in __init__
  File "/home/harry/oak-tutorial/oak-env/lib/python3.9/site-packages/oaklib/implementations/pronto/pronto_implementation.py", line 73, in __post_init__
    ontology = Ontology.from_obo_library(resource.slug)
  File "/home/harry/oak-tutorial/oak-env/lib/python3.9/site-packages/pronto/ontology.py", line 206, in from_obo_library
    return cls(
  File "/home/harry/oak-tutorial/oak-env/lib/python3.9/site-packages/pronto/ontology.py", line 283, in __init__
    cls(self).parse_from(_handle)  # type: ignore
  File "/home/harry/oak-tutorial/oak-env/lib/python3.9/site-packages/pronto/parsers/rdfxml.py", line 115, in parse_from
    self._extract_annotation_property(prop, curies)
  File "/home/harry/oak-tutorial/oak-env/lib/python3.9/site-packages/pronto/parsers/rdfxml.py", line 668, in _extract_annotation_property
    label = elem.find(_NS["rdfs"]["label"]).text
AttributeError: 'NoneType' object has no attribute 'text'

remove print statements in tests

switch to logging.output -- and include more tests on the output

Add a command for structurally comparing two ontology based on an SSSOM mapping set

inputs: O1, O2, Mappings

Extract from O1 the set of terms used in mappings, perform gap-fill to obtain non-redundant inferred relationships between all mapped terms

for each relationship, compare with matched relationship in O2. Categorize as

identical, asserted
identical, inferred on either or both sides
different relationship (e.g. switches from is-a to part-of)
invalid (may require dynamic reasoning so many implementations may not implement this part)

actions take too long

0.2.0 release things to be decided

switch label to lbl #26
use iterators ubiquitously?
One CLI with many subcommands, or subcommands partitioned across different CLIs
package structure
CLI: runoak vs claiming oak

Implement gap filling for subsets

From @dosumis:

The graph is seeded with 2 terms and an objectProperty and show a large set of related terms and their relationships. I want only relationships between the terms specified, via subClassOf + some set of OP existential restrictions

Here's an example from HubMap - the seed = a set of terms + BFO:0000050. Only terms in the seed are in the graph. A non-redundant set of part_of and subClassOf relationships are shown

I think this is more or less the same as: ontodev/robot#497

SQLImpl() does not download ontology?

from oaklib.resource import OntologyResource
from oaklib.implementations.sqldb.sql_implementation import SqlImplementation
resource = OntologyResource(slug='mondo.obo', local=False)
oi = SqlImplementation(resource)

results in:

ArgumentError: Could not parse rfc1738 URL from string 'mondo.obo'

Same works with prontoimpl

Create table of implementation x interface/method

from @dosumis

notes:
"We need a table that shows which operations are suitable for which source
ubergraph does not work with “tree”
"

Test with sssom schema

See linkml/linkml#797

We want to make sure everything still works when sssom starts importing sssom_schema

Document outputs more in tutorial

part1 relies on some understand of basic unix CLI philosophy

considering adding basic examples of piping and redirecting

Also explain --output and --output-format up-front

extract-triples sometimes leaves owl axioms incomplete leading to ErrorNs in owlapi

To replicate:

runoak -i ubergraph:uberon extract-triples UBERON:0001463 -o finger1.ttl -O ttl

the ttl looks OK at first, but if we visualize:

runoak -i finger1.ttl viz UBERON:0001463 -p i,p

we get truncated graphs

in protege:

under manus we have:

    rdfs:subClassOf [ a owl:Restriction ;
            owl:onProperty ns1:RO_0002551 ;
            owl:someValuesFrom ns1:UBERON_0001442 ],
        [ a owl:Restriction ;
            owl:onProperty ns1:RO_0002202 ;
            owl:someValuesFrom ns1:UBERON_0006875 ] ;
    owl:equivalentClass [ ] ;

for some reason the subclass axiom isn't extracted, and the equivalence axiom is to a blank node

Finalize naming conventions and method signatures for all interfaces

Add example of how to do gene set enrichment

Docs example fails: `runoak validate -i obolibrary:mondo.obo terms`

Description

Hello all. Glad to be finally starting to use OAK.

I'm just playing around with some options, and this first example that I took from the README.md didn't work.

Error

Error: No such option: -i

Log

runoak validate -i obolibrary:mondo.obo terms
Usage: runoak validate [OPTIONS]
Try 'runoak validate --help' for help.

Error: No such option: -i

Support for reasoning

Strategies:

owlery #31
owlapi interaction e.g via robot-python plugin
- partial: https://github.com/INCATools/oakx-robot
async approach - separate process writes to common store
native python, or python wrapping rust

Note that for static ontologies when using either

sql_implementation
ubergraph

We get pre-reasoned relation graph results already

fix typo in tutorial for input option

Reported by @shawntanzk

-input should be --input in tutorial

Lexmatch only creates skos:closeMatch?

Is there currently any documentation on the lexmatch code?

I noticed that currently everything in lexmatch get skos:closeMatch:

DOID:0050140	acute diarrhea	skos:closeMatch	SYMP:0000675	acute diarrhea	Lexical	oaklib	rdfs:label	rdfs:label	acute diarrhea

OAK command:

runoak -i DLO.obo lexmatch -o DLO.ssom.tsv

This gives the following error:

/Users/marcin/Documents/ontology/OAK/ontology-access-kit/venv/lib/python3.9/site-packages/pronto/parsers/rdfxml.py:286: SyntaxWarning: <Element '{http://purl.org/dc/elements/1.1/}description' at 0x7fca5a2b2cc0> contains text but no `xsd:datatype`
  meta.annotations.add(self._extract_literal_pv(child))
/Users/marcin/Documents/ontology/OAK/ontology-access-kit/venv/lib/python3.9/site-packages/pronto/parsers/rdfxml.py:286: SyntaxWarning: <Element '{http://purl.org/dc/elements/1.1/}title' at 0x7fca5a2b2d60> contains text but no `xsd:datatype`
  meta.annotations.add(self._extract_literal_pv(child))
/Users/marcin/Documents/ontology/OAK/ontology-access-kit/venv/lib/python3.9/site-packages/pronto/ontology.py:283: NotImplementedWarning: cannot process plain `owl:AnnotationProperty`
  cls(self).parse_from(_handle)  # type: ignore

To reproduce, the DLO input files are here:
DLO.xrdf
DLO.obo

lexmatch should create a legal sssom file

Currently I notice these violations:

License and mapping set ids should be purls (@hrshdhgd we can use what we use as defaults in sssom-py as well)
no curie map (we should be able to pass in a metadata parameter just as in sssom py)
Some subject_id/obect_id values are not curies presumable because they are not known w/o a curie map

extend bioportal_implementation to implement get_sssom_mappings_by_curie

You can use the ols_implementation as a guide. Consult with @hrshdhgd with any questions about the SSSOM datamodel.

Also add a test to test_bioportal for this

This will be used by mapping-walker

@pkalita-lbl you should have an invite to this repo, can you assign yourself, thanks!

get_translations(curie, property)

Alternatively this could just be woven into existing interfaces. Note that all sparql impls have:

    multilingual: bool = None
    preferred_language: LANGUAGE_TAG = field(default_factory=lambda: "en")

this is used to determine the default language if the triplestore supports multiple languages

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