Comments (9)
From @cmungall on March 15, 2015 1:1
@tudorgroza not sure I understand these files
why is this one in 1-n?
D013724 (Teratoma) :: [0005566, 0005563, 0003307]
Mappings highlighted:
/ DOID:4 ! disease
is_a DOID:14566 ! disease of cellular proliferation
is_a DOID:162 ! cancer
is_a DOID:0050687 ! cell type cancer
is_a DOID:2994 ! germ cell cancer
is_a DOID:3095 ! germ cell and embryonal cancer
is_a DOID:3307 ! teratoma ***
is_a DOID:2660 ! cystic teratoma
is_a DOID:5563 ! malignant teratoma ***
is_a DOID:5565 ! adult teratoma
is_a DOID:5566 ! mature teratoma ***
is_a DOID:5567 ! ovarian germ cell teratoma
I guess this is just because mesh has dodgy synonyms?
btw, not all DOIDs are zero-padded, annoyingly
from monarch-disease-ontology-retired.
From @cmungall on March 15, 2015 1:5
These are the meshes in the list that I didn't find DO mappings for
Should see if @tudorgroza maps some I don't
Then pass to DO folks for addition?
from monarch-disease-ontology-retired.
From @mellybelly on March 15, 2015 1:41
Should all MeSH diseases (or at least the union of those from CTD file and common disease work) have an xref in DO? do we need this so as to not use MeSH directly? what if a MeSH term maps to a DC term but not a DO term? There are a lot of unmatched terms there, though I do see a few that likely didn't match due to not exact string.
For example, 'adult T-cell leukemia' in DO has exact synonym 'Adult T-cell leukemia/lymphoma' which matches to MeSH 'Lymphoma, T-Cell' on your list of unmatched terms. The DO term has an xref to the NCI term 'Adult T-Cell Leukemia/Lymphoma' (Code C3184).
(though DO's use of exact synonyms is perhaps a bit greedy)
from monarch-disease-ontology-retired.
From @tudorgroza on March 15, 2015 4:20
@cmungall that mapping comes from DO (originally in the format DOID:0005566::D013724 | DOID:0005563::D013724 | DOID:0003307::D013724) and hence I assume the DO people tried to relate terms at different levels of specificity (i.e., the more specific DO terms to the more general MeSH term).
W.r.t. the padding - is there something I can do to fix it?
from monarch-disease-ontology-retired.
From @tudorgroza on March 15, 2015 4:35
@cmungall I couldn't find additional mappings for the list you've compiled there.
from monarch-disease-ontology-retired.
From @cmungall on March 15, 2015 23:42
@tudorgroza - I see, those were the xrefs already in DO. My list should subsume these.
@mellybelly the CTD list subsumes mesh_list.txt, with the exception of MESH:D012203 Rh isoimmunization, which is in DO already as an xref so we don't need an extra class
from monarch-disease-ontology-retired.
From @cmungall on March 17, 2015 4:55
Didn't remember to tag the commit, but mondo now has mesh classes, either as equivalents to existing mondo classes, or sometimes as their own class with subclass axioms to existing mondos.
This can lead to some oddities, e.g.
[Term]
id: MESH:D004806
name: Ependymoma
is_a: DOID:5075 ! myxopapillary ependymoma
is_a: DOID:5500 ! cellular ependymoma
is_a: DOID:5505 ! papillary ependymoma
is_a: DOID:5507 ! clear cell ependymoma
is_a: DOID:5889 ! DOID:5889
because there is no generic ependymoma in mondo. But this is better than alternatives
from monarch-disease-ontology-retired.
From @cmungall on March 18, 2015 21:15
Adding MESH causes real problems. Leaving aside the weird junk it brings in, it artificially inflates the diseases we care about
For example, in the latest build we have distinct entries:
[Term]
id: OMIM:602404
name: Parkinson Disease 3, Autosomal Dominant
namespace: MGI_disease_ontology
synonym: "PARK3" EXACT []
synonym: "PARKINSON DISEASE 3, AUTOSOMAL DOMINANT; PARK3" EXACT []
is_a: DOID:14330 ! Parkinson's disease
is_a: DOID:630 ! genetic disease
is_a: Orphanet:2828 ! Young adult-onset Parkinsonism
[Term]
id: MESH:C537176
name: Parkinson disease 3
is_a: MESH:D010300 ! Parkinson Disease
it makes a mess of the PD graph:
It's not as easy to merge entries like this as it seems, but I'll try.
However, I'd rather get rid of MESH and map CTD diseases upfront
from monarch-disease-ontology-retired.
From @cmungall on March 18, 2015 21:52
Disregard my previous comment. Was not aligning mesh to the correct target. Fixed this. PD graph now looks better (stll oddities from ordo, but at least all mesh is now tucked in with the relevant OMIM or DOID or Orphanet class). Hmm, PD3 is still a problem. But at least the others mostly are incorporated correctly.
from monarch-disease-ontology-retired.
Related Issues (20)
- Inheritance type inconsistencies HOT 3
- ORDO: Autosomal dominant non-syndromic intellectual disability is classified as etiological subtype HOT 3
- ORDO: X-linked nonsyndromic deafness HOT 5
- rhabdoid cancer HOT 1
- potential Legacy_Concept_Name issues from NCIT (Fanconi Anemia vs Syndrome)
- loose classes? HOT 2
- ORDO: Text definitions sometimes truncated HOT 8
- Orphanet disease IDs without classification and not in ORDO HOT 1
- Genetic hypertension is_a renal disease? HOT 1
- ORDO constitutional vs acquired alplastic anemia HOT 1
- familial isolated restrictive cardiomyopathy HOT 1
- Orpha vs Orphanet HOT 5
- Self loop for MONDO:0010765 HOT 2
- Anti-NMDA Receptor Encephalitis HOT 10
- Missing Orphanet Diseases HOT 4
- Retinoblastoma: hereditary or non hereditary HOT 1
- Some disease description text has strange references embedded HOT 1
- Report on metrics since 2016-09-01 HOT 1
- GO import outdated, causing unspecified reasoning behaviour HOT 1
- Move issues from here to new repo, or close them HOT 2
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from monarch-disease-ontology-retired.