Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Map/curate 344 EFO measurement branch terms to OBA traits #276

Closed
2 tasks done
rays22 opened this issue Jul 31, 2023 · 7 comments · Fixed by #293 or #295
Closed
2 tasks done

Map/curate 344 EFO measurement branch terms to OBA traits #276

rays22 opened this issue Jul 31, 2023 · 7 comments · Fixed by #293 or #295
Assignees
@rays22
Labels
gwas trait

Comments

@rays22
Copy link
Contributor

rays22 commented Jul 31, 2023 •
edited
Loading

  • Map EFO measurement branch terms to OBA traits
  • Create new OBA trait terms as needed

Related to
#162 (comment)
@rays22 rays22 self-assigned this Jul 31, 2023
@rays22
Copy link
Contributor Author

rays22 commented Jul 31, 2023 •
edited
Loading

First : curate PATO qualities.

@rays22 rays22 changed the title Map/curate 469 EFO measurement branch terms to OBA traits Map/curate 344 EFO measurement branch terms to OBA traits Aug 1, 2023
@rays22
Copy link
Contributor Author

rays22 commented Aug 3, 2023

Mapping table: https://docs.google.com/spreadsheets/d/1YXwgzdZ4dSxfDpipfjfxNsw3uJGB_wNsbxRHUwsgVdk/edit#gid=1050615924

@rays22
Copy link
Contributor Author

rays22 commented Aug 4, 2023

  • Examples of different ways of measuring the same trait, or different statistical attributes of a variable trait.
id label entity entity label quality quality label location location label mapping predicate
EFO:0004528 mean corpuscular hemoglobin concentration CHEBI:35143 hemoglobin PATO:0000070 amount CL:0000232 erythrocyte skos:exactMatch
EFO:0009202 Reticulocyte Mean Corpuscular Hemoglobin Measurement CHEBI:35143 hemoglobin PATO:0000070 amount CL:0000558 reticulocyte skos:exactMatch
EFO:0009204 Corpuscular Hemoglobin Concentration Distribution Width CHEBI:35143 hemoglobin PATO:0001303 variability CL:0000232 erythrocyte skos:exactMatch
EFO:0009205 Corpuscular Hemoglobin Content CHEBI:35143 hemoglobin PATO:0000070 amount CL:0000232 erythrocyte skos:exactMatch
EFO:0009228 Reticulocyte Corpuscular Hemoglobin Concentration Mean CHEBI:35143 hemoglobin PATO:0000070 amount CL:0000558 reticulocyte skos:exactMatch
EFO:0009229 Reticulocyte Corpuscular Hemoglobin Content CHEBI:35143 hemoglobin PATO:0000070 amount CL:0000558 reticulocyte skos:exactMatch
EFO:0009230 Reticulocyte Corpuscular Hemoglobin Distribution Width CHEBI:35143 hemoglobin PATO:0001303 variability CL:0000558 reticulocyte skos:exactMatch
EFO:0009231 Reticulocyte Hemoglobin Distribution Width CHEBI:35143 hemoglobin PATO:0001303 variability CL:0000558 reticulocyte skos:exactMatch

@matentzn
Copy link
Contributor

matentzn commented Aug 4, 2023

We are not creating trait terms for statistical measures I assume?

@rays22
Copy link
Contributor Author

rays22 commented Aug 4, 2023

We are not creating trait terms for statistical measures I assume?

No, that is not my intention. I want to map the 9 measurement terms above to 4 traits:

entity entity label quality quality label location location label
CHEBI:35143 hemoglobin PATO:0000070 amount CL:0000232 erythrocyte
CHEBI:35143 hemoglobin PATO:0000070 amount CL:0000558 reticulocyte
CHEBI:35143 hemoglobin PATO:0001303 variability CL:0000232 erythrocyte
CHEBI:35143 hemoglobin PATO:0001303 variability CL:0000558 reticulocyte

@matentzn
Copy link
Contributor

matentzn commented Aug 4, 2023

Very good!

@rays22
Copy link
Contributor Author

rays22 commented Aug 4, 2023

  • Progress so far:
class to be defined predicate defined_class_name entity entity_name attribute attribute_name location location_name exact_synonyms
EFO:0010759 skos:exactMatch male reproductive system attribute UBERON:0000079 male reproductive system PATO:0000001 quality none #N/A  
EFO:0004464 skos:exactMatch brain attribute UBERON:0000955 brain PATO:0000001 quality none #N/A  
EFO:0004550 skos:exactMatch amygdala reactivity attribute GO:0050896 response to stimulus PATO:0000001 quality UBERON:0001876 amygdala  
EFO:0004782 skos:exactMatch behaviour attribute GO:0007610 behavior PATO:0000001 quality none #N/A  
EFO:0007021 skos:exactMatch Lewy body attribute GO:0097413 Lewy body PATO:0000001 quality none #N/A  
EFO:0007716 skos:exactMatch carotid artery attribute UBERON:0005396 carotid artery segment PATO:0000001 quality none #N/A  
EFO:0007738 skos:exactMatch cingulate cortex attribute UBERON:0003027 cingulate cortex PATO:0000001 quality none #N/A  
EFO:0007786 skos:exactMatch menstrual cycle attribute GO:0044850 menstrual cycle PATO:0000001 quality none #N/A  
EFO:0008375 skos:exactMatch macula attribute UBERON:0000054 macula PATO:0000001 quality none #N/A  
EFO:0008389 skos:exactMatch putamen attribute UBERON:0001874 putamen PATO:0000001 quality none #N/A  
EFO:0008420 skos:exactMatch parietal cortex attribute UBERON:0016530 parietal cortex PATO:0000001 quality none #N/A  
EFO:0010079 skos:exactMatch corneal endothelial cell attribute CL:0000132 corneal endothelial cell PATO:0000001 quality none #N/A  
EFO:0010128 skos:exactMatch immunoglobulin isotype switching measurement GO:0045190 isotype switching PATO:0001236 process quality none #N/A  
EFO:0007772 skos:closeMatch calcaneal bone quantitative ultrasound measurement UBERON:0001450 calcaneus PATO:0000001 quality none #N/A  
EFO:0007822 skos:exactMatch hair colour measurement UBERON:0001037 strand of hair PATO:0000014 color none #N/A  
EFO:0600084 skos:exactMatch bowel opening frequency GO:0035882 defecation rhythm PATO:0000044 frequency none #N/A  
EFO:0007717 skos:closeMatch carotid artery attribute UBERON:0005396 carotid artery segment PATO:0000051 morphology none #N/A carotid artery geometry attribute
EFO:0010972 skos:exactMatch blood phosphate attribute CHEBI:26020 phosphate PATO:0000070 amount UBERON:0000178 blood  
EFO:0010914 skos:exactMatch fatty acid-binding protein level in adipocyte PR:000025846 fatty acid-binding protein PATO:0000070 amount CL:0000136 fat cell fatty acid-binding protein, adipocyte attribute
EFO:0020373 skos:exactMatch fatty acid-binding protein level in heart PR:000025846 fatty acid-binding protein PATO:0000070 amount UBERON:0000948 heart fatty acid-binding protein, heart attribute
EFO:0009250 skos:exactMatch Prorubricyte Count CL:0000549 basophilic erythroblast PATO:0000070 amount none #N/A Prorubricyte Count
EFO:0009239 skos:exactMatch plasma cell count CL:0000786 plasma cell PATO:0000070 amount none #N/A Mature Plasma Cell Count
EFO:0008301 skos:exactMatch toll-like receptor 4:Lymphocyte antigen 96 complex amount PR:000036003 LY96:TLR4 complex PATO:0000070 amount UBERON:0001062 anatomical entity toll-like receptor 4:Lymphocyte antigen 96 complex attribute
EFO:0009187 skos:broadMatch immature platelet quantity CL:0000233 platelet PATO:0000070 amount none #N/A immature platelet fraction
EFO:0009238 skos:broadMatch Immature Plasma Cell Count CL:0000786 plasma cell PATO:0000070 amount none #N/A  
EFO:0009253 skos:broadMatch immature reticulocyte amount CL:0000558 reticulocyte PATO:0000070 amount none #N/A Immature Reticulocyte Fraction attribute
EFO:0020318 skos:exactMatch dentin matrix acidic phosphoprotein 1 amount PR:000006540 dentin matrix acidic phosphoprotein 1 PATO:0000070 amount UBERON:0001062 anatomical entity dentin matrix acidic phosphoprotein 1 attribute
EFO:0004308 skos:exactMatch leukocyte count CL:0000738 leukocyte PATO:0000070 amount none #N/A  
EFO:0007988 skos:exactMatch myeloid white cell count CL:0000766 myeloid leukocyte PATO:0000070 amount none #N/A myeloid white cell count
EFO:0004528 skos:exactMatch hemoglobin amount in erythrocyte CHEBI:35143 hemoglobin PATO:0000070 amount CL:0000232 erythrocyte corpuscular hemoglobin amount
EFO:0009202 skos:exactMatch reticulocyte corpuscular hemoglobin quantity CHEBI:35143 hemoglobin PATO:0000070 amount CL:0000558 reticulocyte  
EFO:0009204 skos:exactMatch corpuscular hemoglobin variability attribute CHEBI:35143 hemoglobin PATO:0001303 variability CL:0000232 erythrocyte  
EFO:0009205 skos:exactMatch corpuscular hemoglobin content CHEBI:35143 hemoglobin PATO:0000070 amount CL:0000232 erythrocyte  
EFO:0009228 skos:exactMatch reticulocyte corpuscular hemoglobin quantity CHEBI:35143 hemoglobin PATO:0000070 amount CL:0000558 reticulocyte  
EFO:0009229 skos:exactMatch reticulocyte corpuscular hemoglobin content CHEBI:35143 hemoglobin PATO:0000070 amount CL:0000558 reticulocyte  
EFO:0009230 skos:exactMatch reticulocyte corpuscular hemoglobin variability CHEBI:35143 hemoglobin PATO:0001303 variability CL:0000558 reticulocyte  
EFO:0009231 skos:exactMatch Reticulocyte Hemoglobin Distribution Width CHEBI:35143 hemoglobin PATO:0001303 variability CL:0000558 reticulocyte Reticulocyte Hemoglobin Distribution Width
EFO:0004532 skos:exactMatch serum gamma-glutamyl transferase level PR:000001458 glutathione hydrolase 1 proenzyme PATO:0000070 amount UBERON:0001977 blood serum  
EFO:0004536 skos:exactMatch total blood protein mass CHEBI:36080 protein PATO:0000125 mass UBERON:0000178 blood total blood protein amount
EFO:0004741 skos:exactMatch blood urea nitrogen level CHEBI:16199 urea PATO:0000070 amount UBERON:0000178 blood  
EFO:0004749 skos:exactMatch C-C motif chemokine 2 level PR:000002122 C-C motif chemokine 2 PATO:0000070 amount UBERON:0001062 anatomical entity CCL2 level
EFO:0004764 skos:exactMatch adipose tissue quantity UBERON:0001013 adipose tissue PATO:0000070 amount none #N/A  
EFO:0004765 skos:exactMatch visceral adipose tissue quantity UBERON:0035818 visceral fat PATO:0000070 amount none #N/A  
EFO:0004864 skos:exactMatch renal sinus adipose tissue quantity UBERON:0001013 adipose tissue PATO:0000070 amount UBERON:0006171 renal sinus  
EFO:0005036 skos:exactMatch platelet quantity CL:0000233 platelet PATO:0000070 amount none #N/A  
EFO:0005193 skos:exactMatch serum IgG glycosylation level GO:0006487 protein N-linked glycosylation PATO:0001236 process quality GO:0071736 IgG immunoglobulin complex, circulating  
EFO:0005653 skos:exactMatch serum metabolite level CHEBI:25212 metabolite PATO:0000070 amount UBERON:0001977 blood serum  
EFO:0005664 skos:exactMatch blood metabolite level CHEBI:25212 metabolite PATO:0000070 amount UBERON:0000178 blood  
EFO:0005760 skos:exactMatch serum carcinoembryonic antigen level PR:000001330 carcinoembryonic antigen-related cell adhesion molecule 5 PATO:0000070 amount UBERON:0001977 blood serum  
EFO:0006920 skos:exactMatch natriuretic peptides B level PR:000011375 natriuretic peptides B PATO:0000070 amount UBERON:0001062 anatomical entity BNP quantity
EFO:0006959 skos:exactMatch gene methylation level GO:0006306 DNA methylation PATO:0000070 amount UBERON:0001062 anatomical entity  
EFO:0007578 skos:exactMatch blood copper level CHEBI:28694 copper atom PATO:0000070 amount UBERON:0000178 blood  
EFO:0007615 skos:exactMatch thrombus formation level UBERON:0010210 blood clot PATO:0000070 amount none #N/A  
EFO:0007657 skos:exactMatch cerebrospinal fluid clusterin level PR:000005615 clusterin PATO:0000070 amount UBERON:0001359 cerebrospinal fluid  
EFO:0007807 skos:exactMatch erythrocyte cadmium level CHEBI:22977 cadmium atom PATO:0000070 amount CL:0000232 erythrocyte  
EFO:0007937 skos:exactMatch blood protein level PR:000000001 protein PATO:0000070 amount UBERON:0000178 blood  
EFO:0007980 skos:exactMatch cerebral blood flow level UBERON:0000178 blood PATO:0002243 fluid flow rate UBERON:0000955 brain  
EFO:0008142 skos:exactMatch granulocyte colony-stimulating factor level PR:000005932 granulocyte colony-stimulating factor PATO:0000070 amount UBERON:0001062 anatomical entity  

rays22 added a commit that referenced this issue Sep 8, 2023
@rays22
Trait terms mapped to EFO measurement classes
0208d1a 
Addresses #276.
@rays22 rays22 mentioned this issue Sep 8, 2023
Merged
rays22 added a commit that referenced this issue Sep 8, 2023
@rays22
Fix duplicate male reproductive system quality term
6e5d7bd 
Addresses #276.
rays22 added a commit that referenced this issue Sep 8, 2023
@rays22
Refresh merged imports
e909326 
and remove duplicate class.

Addresses #276.
@rays22 rays22 mentioned this issue Sep 14, 2023
Open
rays22 added a commit that referenced this issue Sep 27, 2023
@rays22
Update the entity_attribute DOS-DP data table
f52014f 
This commit intends to update the entity_attribute DOS-DP data table.

If applied, this commit will fix #276.
@rays22 rays22 mentioned this issue Sep 27, 2023
Merged
rays22 added a commit that referenced this issue Sep 27, 2023
@rays22
Update response_to_chemical_with_role_stimulus
ae60c78 
Update data table response_to_chemical_with_role_stimulus.tsv
If applied, this commit will fix #276.
rays22 added a commit that referenced this issue Sep 27, 2023
@rays22
Update response_to_chemical_stimulus_trait table
7745b51 
Update data table response_to_chemical_stimulus_trait.tsv

If applied, this commit will fix #276.
rays22 added a commit that referenced this issue Sep 27, 2023
@rays22
Update entity_attribute_location.tsv table
cbec9a4 
Update data table entity_attribute_location.tsv

If applied, this commit will fix #276.
@rays22 rays22 reopened this Oct 13, 2023
@rays22 rays22 mentioned this issue Oct 13, 2023
Merged
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@rays22 rays22

Labels
gwas trait
Projects
@rays22's triage and progress
Status: Done
Milestone
No milestone
2 participants
@matentzn @rays22