microbiomedata nmdc-ontology issues

microbiomedata / nmdc-ontology

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subset with OAK not SPARQL (for LLM training)

#69 turbomam opened 6 months ago
0
LLM scripts intermediate files makefile targets and outputs

#68 turbomam opened 6 months ago
1
Make `experimental_factor` `multivalued` with a range of `ControlledIdentifiedTermValue`

#67 turbomam opened 6 months ago
1
prepare changesheets for problematic triads in MongoDB

#66 turbomam opened 7 months ago
9
ask claude to generate OAK or SPARQL queries; or justifications for it's responses

#65 turbomam opened 7 months ago
0
provide claude with negative examples

#64 turbomam opened 7 months ago
0
feed back discovered MIxS/EnvO etc subsets back into this ontology

#63 turbomam opened 7 months ago
0
Bill Duncan as an author

#62 turbomam closed 7 months ago
1
LLM tools should embed data X from a file but iterate over data Y

#61 turbomam opened 7 months ago
0
LLM scripts should save to a file not print to console

#60 turbomam opened 7 months ago
0
add data assets and prepare for local/.env

#59 turbomam closed 7 months ago
0
Add Bill as an author in `pyproject.toml`

#58 turbomam opened 7 months ago
2
tidy up robot remove output

#57 turbomam closed 7 months ago
0
Save scripts etc for LLM alignment of MIxS and EnvO terms in this repo

#56 turbomam closed 7 months ago
0
remove role cycle

#55 turbomam closed 7 months ago
0
Now that we're importing ontology base versions, do extracts to get labels and heriarcy for `owl:Things`?

#54 turbomam opened 7 months ago
0
import base ontologies if possible

#53 turbomam closed 7 months ago
0
detection of cycles

#52 turbomam closed 7 months ago
0
Modify imports merging to use 'base' artifacts?

#51 turbomam closed 7 months ago
0
Use robot mirroring to make iterative builds of this ontology faster?

#50 turbomam opened 7 months ago
6
subClassOf cycles in nmdco-classes.json breaks the nmdc-server ingest

#49 turbomam closed 7 months ago
1
document how to deploy an OLS instance (locally or on SPIN)

#48 turbomam opened 7 months ago
0
new extract/import in nmdco.Makefile

#47 turbomam closed 7 months ago
0
Add `UBERON:0001153` 'caecum' and `UBERON:0035118` 'material entity in digestive tract' and release

#46 turbomam closed 7 months ago
0
add in classes from qc-reports/problematic_triad_summary.yaml as appropriate

#45 turbomam opened 7 months ago
1
no relation graph

#44 turbomam closed 7 months ago
5
stream pool etc 2023-08-25T12:17:42.901Z

#43 turbomam closed 8 months ago
0
rebuild after fixing dates in EnvO

#42 turbomam closed 8 months ago
0
see problematic_triad_* files for FMA problems

#41 turbomam closed 8 months ago
0
minimized tool.poetry.dependencies

#40 turbomam closed 8 months ago
0
problematic env_braod_scale and env_material

#39 turbomam closed 8 months ago
0
report all invalid biomes and environmental mediums

#38 turbomam closed 8 months ago
0
What is 'root node', `http://purl.obolibrary.org/obo/NMDCO_00000000` and why isn't it the root?

#37 turbomam closed 7 months ago
3
sorted table of NMDCO EnvO classes

#36 turbomam closed 8 months ago
0
Decrease the number of methods used for QC

#35 turbomam opened 8 months ago
0
report of EnvO classes in NMDCO by id owner

#34 turbomam closed 8 months ago
0
DO NOT MERGE remove or modify usages of non redundant relation graph output

#33 turbomam closed 7 months ago
0
remove or modify usages of "non-redundant" relation-graph output

#32 turbomam closed 7 months ago
3
download don't build released envo.db

#31 turbomam closed 8 months ago
0
use `semsql download` to download released envo.db instead of building it

#30 turbomam closed 8 months ago
0
report/count name correction

#29 turbomam closed 8 months ago
0
reports by robot not python

#28 turbomam closed 8 months ago
0
data-vs-ontology-reports

#27 turbomam closed 8 months ago
0
get a report of envo terms with ids in the range of nmdc or nmdc contributors

#26 turbomam closed 8 months ago
0
get a report of EnvO terms with ids in the range of NMDC or NMDC contributors

#25 turbomam closed 8 months ago
0
more informative count table headers

#24 turbomam closed 8 months ago
0
triad and term reports

#23 turbomam closed 8 months ago
0
Identify what terms need to be included in this ontology by querying the NMDC database

#22 turbomam closed 8 months ago
1
make a release

#21 turbomam closed 8 months ago
0
make a release

#20 turbomam closed 8 months ago
0