obophenotype upheno-dev issues

obophenotype / upheno-dev

Framework for the automated construction of uPheno 2.0

MIT License

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For comparison only: DEV branch

#61 matentzn opened 5 months ago
0
ZP to seven digits

#59 matentzn closed 6 months ago
0
Urgent: check why some terms are missing from uPheno 2

#58 matentzn closed 6 months ago
1
upheno_id_map.txt -> some ids have non existent patterns in it

#57 matentzn closed 7 months ago
2
Ols4test

#56 jamesamcl closed 7 months ago
0
Duplicate class label: "abnormality of anatomical entity physiology"

#55 caufieldjh opened 10 months ago
1
DataFrame error in pipeline

#54 jamesamcl opened 1 year ago
0
Add custom upheno lexical pipeline to phenio-utils

#53 matentzn opened 1 year ago
0
update yaml.load usage in lib.py

#52 jamesamcl closed 1 year ago
0
Phenio toolkit

#51 souzadevinicius opened 1 year ago
0
Create repeatable pipeline for generic upheno matches

#50 souzadevinicius closed 6 months ago
1
Create generic patterns on all remaining object properties

#49 souzadevinicius opened 1 year ago
0
tsv files of matches - DO NOT MERGE

#48 rays22 opened 1 year ago
0
Add a pipeline for matching DOSDP pattern files

#47 matentzn opened 1 year ago
1
Lexical matching pipeline

#46 matentzn opened 1 year ago
0
upheno-dev cookiecutter template

#45 matentzn closed 1 year ago
0
Create lexmatch using `oaklib`

#44 hrshdhgd opened 1 year ago
1
Add OAK matching to uPheno 2

#43 matentzn opened 1 year ago
10
HP vs MP special cases

#42 caufieldjh opened 1 year ago
7
Add some kind of anti slim approach for upheno classes that should be skipped by semantic similarity

#41 matentzn opened 1 year ago
0
uPheno 2 review

#40 matentzn opened 1 year ago
5
Create a Monarch Data Science library

#39 matentzn opened 1 year ago
0
Provide instructions to create equivalence model of uPheno after the fact

#38 matentzn opened 1 year ago
0
Update pattern suggestion pipeline

#37 rays22 closed 2 years ago
0
Create a version of HP/MP/ZP that contains _only_ unmatched definitions

#36 matentzn opened 2 years ago
0
uPheno 2 should mirror _all_ phenotypes

#34 matentzn opened 2 years ago
1
uPheno species independent layer needs to be enriched with SSPO synonyms

#35 matentzn opened 2 years ago
0
PLANA_0007536 is both a property and a class/individual

#33 marius-mather opened 2 years ago
1
Old monarch Jenkins pipeline in case needed

#32 matentzn opened 2 years ago
0
Pipeline to suggest new patterns

#31 matentzn closed 1 year ago
5
Different sizes between HP-MP and HP-ZP mappings

#30 liulizhi1996 opened 3 years ago
1
Problems when inferring human gene-phenotype associations from model organism by sequence orthology

#29 liulizhi1996 closed 3 years ago
1
Missing phenotypic orthologues

#28 matentzn opened 3 years ago
0
Switch owlsim data url

#27 kshefchek closed 4 years ago
0
Public uPheno2 (Alpha) review

#26 matentzn opened 4 years ago
7
Find obo file to calculate semantic similarity between MPO and HPO terms

#25 frequena opened 4 years ago
24
DO NOT MERGE: just compare

#24 matentzn opened 4 years ago
0
DO NOT MERGE: Just compare (16GB)

#23 matentzn opened 4 years ago
0
DO NOT MERGE: Just for comparison

#22 matentzn opened 4 years ago
0
Ensure appropriate Metadata on final ontology artefacts

#21 matentzn opened 4 years ago
0
Remove replace_owl_thing_in_tsvs from pipeline

#20 matentzn opened 4 years ago
0
Update abnormalQualityOfThing.tsv

#19 nicolevasilevsky closed 4 years ago
0
uPheno 2: Alpha review

#18 matentzn opened 4 years ago
5
Maintain the cross-species mappings TSVs as part of release (alpha)

#17 matentzn opened 4 years ago
0
Ensure that there is no "rogue" terms on the top level of the class hierarchy (under thing)

#16 matentzn opened 4 years ago
0
Handle the mapping of the old ID*PHENOTYPE terms to new system

#15 matentzn opened 4 years ago
1
Ensure basic phenotype classification

#14 matentzn opened 4 years ago
0
Review UPHENO id generation

#13 matentzn opened 4 years ago
0
Ensure all anatomy falls under UBERON:anatomical entity

#12 matentzn opened 4 years ago
0
Output suggests that phenotype components are not classified with reasoner

#11 matentzn opened 4 years ago
0