unfortunately there is a bug in OE that allows you to define subsets with spaces in the subset ID. This causes problems for some parsers.

can you change:

subsetdef: sexually transmitted infectious disease "sexually transmitted"

to

subsetdef: sexually_transmitted_infectious_disease "sexually transmitted"

you may also want to make the label track the ID. this isn't required but it's standard practice.

subsetdef: sexually_transmitted_infectious_disease "sexually transmitted infectious disease"

you will also have to fix the subset tags. E.g.:

perl -npe 's/subset: sexually transmitted infectious disease/subset: sexually_transmitted_infectious_disease/' HumanDO.obo

Reported by: cmungall

Original Ticket: diseaseontology/feature-requests/18

[Diseaseontology-discussion] Colorectal Cancer, Liver Cancer, DO-slim?
Delete From: <peili_zhang@vr…> – 2008-05-20 15:17

when we query for ‘liver cancer’, we’d like to see both
‘primary liver cancer’ and ‘metastatic liver cancer’ among its children.
however, in DO, ‘liver metastases’ and ‘Adult Primary Liver Cancer’ only
converge to ‘Malignant neoplasm of liver and intrahepatic bile ducts’ if
we go up 2 and 4 levels from the two nodes, respectively.

Peili Zhang, Ph.D.
Vertex Pharmaceuticals, Inc.
130 Waverly Street
Cambridge, MA 02139
617-444-6593

Reported by: lschriml

Original Ticket: diseaseontology/feature-requests/2

Hi,
In the fission yeast database we flag pombe-genes which have disease-associated orthologs in higher eukaryotes. We currently supply these in a free-text format but we thought we'd convert them into a controlled vocabulary.

I could find the DO terms for most of the genes, however a few appear to be missing and I'd like to request these terms. I've tried to supply some means of a reference to the disease - and apologies in advance if I've made some suggestions that aren't in the scope of DO - I do not have a background in disease.

Many thanks,
Antonia.

4-hydroxybutyricaciduria ref: http://en.wikipedia.org/wiki/Succinic\_semialdehyde\_dehydrogenase\_deficiency

amyotrophic lateral sclerosis type 8 (child of DOID:332)

adenylosuccinase lyase deficiency ref http://en.wikipedia.org/wiki/Adenylosuccinate\_lyase\_deficiency

ARC syndrome (Arthrogryposis–renal dysfunction–cholestasis) http://en.wikipedia.org/wiki/Arc\_syndrome

Armfield syndrome

Ataxia with oculomotor apraxia type 1 (child of DOID:0060135 ?) http://www.ncbi.nlm.nih.gov/books/NBK1456/

Ataxia with oculomotor apraxia type 2 ref: http://www.ncbi.nlm.nih.gov/books/NBK1154/

Batten disease synonym: juvenile neuronal ceroid lipofuscinosis child of:DOID:14503 ref:http://en.wikipedia.org/wiki/Batten%27s\_Disease

Chorea-acanthocytosis ref: http://en.wikipedia.org/wiki/Chorea\_acanthocytosis

Deafness-dystonia syndrome child of DOID:5159 ref: http://en.wikipedia.org/wiki/TIMM8A

Metabolic acidosis parent of DOID:3650 ref: http://en.wikipedia.org/wiki/Metabolic\_acidosis

Midface dysplasia

Mitochondrial complex V (ATP synthase) deficiency, nuclear type 1 http://omim.org/entry/604273

Myotonic dystrophy type 2 - child of DOID:11722. For the term DOID:11722 Steinert's disease is listed as a synonym but this is actually type 1 and should therefore be a child.

N syndrome ref: http://omim.org/entry/310465

Polycystic liver disease (PLD) OMIM 174050 http://en.wikipedia.org/wiki/Polycystic\_liver\_disease

phaeochromocytoma OMIM 171300

Paroxysmal nocturnal hemoglobinuria OMIM 300818

Paraganglioma MeSH D010235

paramyloidosis child of DOID:9120, ref: http://www.mondofacto.com/facts/dictionary?paramyloidosis

Rapadilino syndrome OMIM 266280 http://en.wikipedia.org/wiki/Rapadilino\_syndrome

Schneckenbecken dysplasia OMIM 269250

X-linked myopathy with excessive autophagy (XMEA) ref:PMID:10757644 child of DOID:423

X-linked non-specific mental retardation ref: PMID:9668174

Reported by: antonialock

Original Ticket: diseaseontology/feature-requests/29

When I try loading the latest OWL version in Protege 4.1 beta, I get the following error, both when I save the OWL file locally and open it, and when I load it from a URI:

org.semanticweb.owlapi.rdf.syntax.RDFParserException: [line=420:column=96] IRI 'http://purl.org/obo/owl/obo\#zoonotic infectious disease' cannot be resolved against curent base IRI http://purl.org/obo/owl/disease\_ontology

Reported by: *anonymous

Original Ticket: diseaseontology/feature-requests/19

We are curating a model of Spinocerebellar ataxia type 5 (SCA5) OMIM:600224 based on PMID:20368622.

Currently, OMIM:600224 is listed as a dbxref for the general sounding DO term spinocerebellar ataxia ; DOID:1441. However, SCA5 is caused by deletions/missense mutations in SPTBN2 rather than expanded CAG repeats so isn't consistent with the DO definition "A spinocerebellar degeneration that has_material_basis_in expanded CAG triplet repeats resulting in spinal cord and cerebellum degeneration."

Looks like the general term needs a less specific definition to be able group these conditions and SCA5 should possibly be a separate term?

At present there are only 5 children of DOID:1441 but OMIM has a 'phenotypic series' consisting of 33 types of spinocerebellar ataxia. As the current DO children of DOID:1441 are all undefined it isn't clear why some have a entry in their own right rather than being linked to the general parent. It would be great if these could be reviewed at some point to add defs and ensure that all that merit a separate entry have one. I'm guessing this might not be straightforward in terms of classification. I also noticed that OMIM:615386 SCAR14 (also caused by mutation in SPTBN2) is not included as a dbxref in DO (I haven't checked all 33!).

Reported by: stweedie

Original Ticket: diseaseontology/feature-requests/50

Lynn, hope you are well. I'm requesting the term 'Perrault syndrome' (human gene implicated is LARS2). Here is the OMIM page:http://omim.org/entry/615300, and the GHR page:http://ghr.nlm.nih.gov/gene/LARS2. I picked you as the 'owner' of the issue rather than leaving it empty, hope that's okay.

Thanks in advance
Ranjana

Reported by: ranjana

Original Ticket: diseaseontology/feature-requests/39

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4062962/pdf/emss-58937.pdf

Discusses pancreatic agenesis. Would it be possible to add a DO term for this disease please?

Reported by: *anonymous

Original Ticket: diseaseontology/feature-requests/45

pref. name is coenzyme Q10

should this be co-enzyme q10 deficiency - definition suggests this name and current label appears to refer to the entitity and not the disposition.

Reported by: parkinso

Original Ticket: diseaseontology/feature-requests/30

Barry initiated discussion on the term 'Disorder' in DO.
DO contains diseases, where the community naming convention is "disorder", e.g. mental health diseases
DO also has an upper level node for congenital diseases: medical disorder

Discussion would be beneficial to figure out the best placement, naming, categorization of these terms.

Barry:
I see that you have made program also with the upper level structure; however, there are also problems, which we need to talk about at
some stage, e.g. in conflicting uses of 'disorder' at different places.

Lynn: -- As you noted, Disorder, is a complex issue for us.
In many areas of Disease research, Disorder is the preferred way to refer to a condition.
Mental Health Diseases are a good example of this community naming convention.
-- We considers these to be a 'disease' although their name is ____ disorder
The medical disorder upper level node which includes congenital diseases bears further discussion certainly.

Reported by: lschriml

Original Ticket: diseaseontology/feature-requests/26

Hi Lynn

Could you add CHARGE syndrome (OMIM:214800)

OMIM summarizes this as 'CHARGE syndrome is characterized by a pattern of congenital anomalies including choanal atresia and malformations of the heart, inner ear, and retina' based on PMID:10590394

I guess the parent is syndrome ; DOID:225

Thanks,
Susan

Reported by: stweedie

Original Ticket: diseaseontology/feature-requests/35

Please consider the following synonym additions:
Creutzfeldt Jakob disease (DOID:11949)
Creutzfeldt-Jakob disease (DOID:11949)
[or correct the two with Jakob spelt Jacob]

coronary heart disease (DOID:3393) [this was removed in a moderately recent change]

I note that quite a few of the synonyms from SNOMED CT end with "(disorder)". Is adding the variant without "(disorder)" as a synonym within the scope of the ontology? [in many cases the synonym that would result from doing so is already present] In a few cases I think removing the qualifier may leave you with an anatomical synonym rather than a disease synonym but in many cases the synonym without the qualifier seems reasonable e.g. DOID:4249

Reported by: dan2097

Original Ticket: diseaseontology/feature-requests/44

Shouldn't mitochondrial myopathy DOID:699 and cardiomyopathy DOID:0050700 also be child terms of myopathy DOID:423?

Reported by: stweedie

Original Ticket: diseaseontology/feature-requests/37

The following pairs share either a name or exact synonym. These should either be merged, or the synonym scope be relegated to something weaker

col1: clashing label
col2: Class1
col3: Class2

spleen disease DOID:0000815-spleen disease DOID:2529-splenic diseases
spleen disease DOID:0000815-spleen disease DOID:2529-splenic diseases
infectious diarrhea DOID:0050006-infectious diarrhea DOID:12384-dysentery
favus DOID:0050109-favus DOID:4336-tinea favosa
gastric leiomyoma DOID:10087-gastric leiomyoma DOID:7495-mouse gastric leiomyoma
gastric hamartoma DOID:10089-gastric hamartoma DOID:10090-mouse gastric hamartoma
chronic leukemia nos DOID:1036-chronic leukemia nos DOID:9145-leukemia of unspecified cell type, chronic
arteriovenous malformation DOID:11294-arteriovenous malformation DOID:466-congenital arteriovenous malformation
arteriovenous malformation DOID:11294-arteriovenous malformation DOID:466-congenital arteriovenous malformation
arteriovenous malformation DOID:11294-arteriovenous malformation DOID:466-congenital arteriovenous malformation
abdominal cancer DOID:122-abdominal cancer DOID:284-malignant neoplasm of abdomen
peripheral nervous system disease DOID:13069-peripheral nervous system disease DOID:574-peripheral nervous system diseases
interstitial cystitis DOID:13949-interstitial cystitis DOID:1678-chronic interstitial cystitis
aortic valve disease DOID:56-aortic valve disease DOID:62-aortic valve disease
central breast papilloma DOID:8224-central breast papilloma DOID:8226-solitary intraductal breast papilloma
inflammatory disease of female pelvic organs and/or tissues DOID:1003-pelvic inflammatory disease DOID:1260-parametritis
gastric lipoma DOID:10085-mouse gastric lipoma DOID:10186-gastric lipoma
benign gastric granular cell tumor DOID:10091-benign mouse gastric granular cell tumor DOID:10092-benign gastric granular cell tumor
potassium deficiency DOID:1010-hypokalemia DOID:13582-potassium deficiency
potassium deficiency DOID:1010-hypokalemia DOID:13582-potassium deficiency
potassium deficiency DOID:1010-hypokalemia DOID:13582-potassium deficiency
potassium deficiency DOID:1010-hypokalemia DOID:13582-potassium deficiency
abscess DOID:103-bacterial abscess DOID:1161-abscess
bpd DOID:10930-borderline personality disorder DOID:11651-bronchopulmonary dysplasia
arteriovenous malformation DOID:11294-arteriovenous malformation DOID:466-congenital arteriovenous malformation
arteriovenous malformation DOID:11294-arteriovenous malformation DOID:466-congenital arteriovenous malformation
arteriovenous malformation DOID:11294-arteriovenous malformation DOID:466-congenital arteriovenous malformation
lymphogranulomatosis DOID:11335-sarcoidosis DOID:8567-hodgkin’s disease, unspecified type
diseases of mitral valve DOID:11505-rheumatic disease of mitral valve DOID:61-diseases of mitral valve
mitral and aortic incompetence (disorder) DOID:11737-mitral incompetence DOID:54-aortic incompetence
mitral and aortic valve regurgitation DOID:11737-mitral incompetence DOID:54-aortic incompetence
mitral valve insufficiency and aortic valve insufficiency DOID:11737-mitral incompetence DOID:54-aortic incompetence
rheumatic mitral and aortic valve regurgitation (disorder) DOID:11737-mitral incompetence DOID:54-aortic incompetence
pectus carinatum DOID:11992-congenital pectus carinatum DOID:12459-congenital funnel chest
pectus carinatum DOID:11992-congenital pectus carinatum DOID:12459-congenital funnel chest
biliary cirrhosis DOID:12236-primary biliary cirrhosis DOID:1851-biliary cirrhosis
biliary cirrhosis DOID:12236-primary biliary cirrhosis DOID:1851-biliary cirrhosis
waterhouse-friderichsen syndrome DOID:12613-waterhouse-friderichsen syndrome, meningococcal DOID:9931-waterhouse-friderichsen syndrome
hav – hallux abductovalgus DOID:12824-acquired hallux valgus DOID:2201-hallux valgus
flat foot DOID:13028-pes planus – acquired DOID:3776-flatfoot
flat foot DOID:13028-pes planus – acquired DOID:3776-flatfoot
flat foot nos DOID:13028-pes planus – acquired DOID:3776-flatfoot
pes planus DOID:13028-pes planus – acquired DOID:3776-flatfoot
impotence DOID:13478-male erectile disorder due to specified medical condition DOID:1875-impotence
impotence DOID:13478-male erectile disorder due to specified medical condition DOID:1875-impotence
interstitial cystitis DOID:13949-interstitial cystitis DOID:1678-chronic interstitial cystitis
macular corneal dystrophy DOID:14315-congenital macular corneal dystrophy DOID:2565-macular corneal dystrophy
macular corneal dystrophy DOID:14315-congenital macular corneal dystrophy DOID:2565-macular corneal dystrophy
fibroadenoma DOID:1618-fibroadenoma of breast DOID:2693-fibroadenoma
laurence-moon-biedl syndrome DOID:1930-laurence-moon syndrome DOID:1935-bardet-biedl syndrome
laurence-moon-biedl syndrome DOID:1930-laurence-moon syndrome DOID:1935-bardet-biedl syndrome
infectious diseases DOID:2040-communicable disease DOID:95-infectious diseases
erysipeloid (disorder) DOID:2470-erysipelothrix infection DOID:2471-infection due to erysipelothrix rhusiopathiae (disorder)
germinoma DOID:2994-germ cell tumor DOID:3304-germinoma
germinoma DOID:2994-germ cell tumor DOID:3304-germinoma
ptosis DOID:347-blepharoptosis DOID:9308-ptosis
pediatric neoplasm DOID:3673-malignant childhood neoplasm DOID:921-pediatric neoplasm
renal cancer DOID:3676-malignant neoplasm of kidney DOID:4451-renal carcinoma
plasma cell neoplasm DOID:3721-plasmacytoma DOID:6536-plasma cell neoplasm
liver disease DOID:409-liver diseases DOID:46-liver disease
liver disease DOID:409-liver diseases DOID:46-liver disease
scleroderma DOID:418-systemic scleroderma DOID:419-scleroderma
scleroderma DOID:418-systemic scleroderma DOID:419-scleroderma
myofibroma DOID:4386-myofibroma (morphologic abnormality) DOID:5203-solitary myofibromatosis
who grade ii astrocytoma DOID:4857-diffuse astrocytoma DOID:7009-adult diffuse astrocytoma
diseases of mitral and aortic valves DOID:56-aortic valve disease DOID:59-mitral valve disease
diseases of mitral and aortic valves DOID:56-aortic valve disease DOID:59-mitral valve disease
diseases of mitral and aortic valves DOID:56-aortic valve disease DOID:59-mitral valve disease
diseases of mitral and aortic valves DOID:56-aortic valve disease DOID:59-mitral valve disease
diseases of mitral and aortic valves (disorder) DOID:56-aortic valve disease DOID:59-mitral valve disease
mitral and aortic valve disease nos (disorder) DOID:56-aortic valve disease DOID:59-mitral valve disease
mitral and aortic valve diseases, unspecified DOID:56-aortic valve disease DOID:59-mitral valve disease
ulcerative stomatitis DOID:9663-aphthous stomatitis DOID:9673-ulcerative stomatitis
ulcerative stomatitis DOID:9663-aphthous stomatitis DOID:9673-ulcerative stomatitis

Reported by: cmungall

Original Ticket: diseaseontology/feature-requests/8

251 synonyms in DO start with [M], 545 with [M] or [X] and a total of 676 start with the grep pattern [[A-Z]]. This was reported by Tomasz Adamusiak at the EBI, reviewed, and the terms removed.

Reported by: wakibbe

Original Ticket: diseaseontology/feature-requests/12

As per the communication from Dr. Peters to Dr.Kibbe, we are providing a master list of disease terms representing all of the human disease (and animal model) data in the IEDB. This will be provided in the form of Excel spreadsheet. We are submitting this in order to request 1) the addition of certain non-existent entities, 2) the modification of disease names, and/or 3) the addition of child nodes under existing DOID parent terms. These requests are highlighted in the spreadsheet. . Columns R, S and T show DOID (identifier), relatioship (parent_identifier) and DO_disease_name. Column "U" provides preferred_disease_name, and in column "W" called "term_status' to indicate what change (if any) is being specifically requested for that entry. Please let contact Kerrie Vaughan with any and all issues. Thank you.

Reported by: *anonymous

Original Ticket: diseaseontology/feature-requests/20

Request on behalf of Lynn Crosby at FlyBase:

OMIM, NIH and others are dropping "'s" for diseases such as Parkinson's, Alzheimer's, Huntington's, etc. Could the variant without the apostrophe s be added as a synonym to each of these cases?

Reported by: *anonymous

Original Ticket: diseaseontology/feature-requests/42

We are having trouble curating with the various dystonia terms. There are two grouping terms ‘dystonia’ and ‘dystonic disease’ - the former is a direct child of ‘nervous system disease’ and the latter is an indirect child of the same term (direct parent is ‘movement disease’). In the absence of definition for these grouping terms we can’t tell what the difference is. It would be very helpful if these could clarify this difference (assuming both terms should be there). GO often add a comment to make users aware when there are similar terms whose usage can be confused and include advice about when to choose one over the other. In fact none of the 8 DO terms with ‘dystonia’ in them have either definitions or OMIM dbxrefs which makes it difficult to use them.

Our immediate problem is finding the most appoprriate term to curate (PMID:15269177) which makes a model of 'early onset torsion dystonia'. From what they say in the introduction, this is the disease caused when human DYT1 is mutated, so the OMIM term for this is DYSTONIA 1, TORSION, AUTOSOMAL DOMINANT; DYT1 (OMIM #128100). It would be good if you could include this OMIM ID under the most appropriate term and add ‘early onset torsion dystonia’ as a synonym. Based on the OMIM article I think this is probably either ‘dystonia musculorum deformans’ or ‘idiopathic familial dystonia’ but we notice there is also ‘symptomatic torsion dystonia’.

Reported by: stweedie

Original Ticket: diseaseontology/feature-requests/36

The def currently says "...two mutated copies of the gene, both of which must be presetn in order for the disease..."

presetn should be present

Reported by: doughowe

Original Ticket: diseaseontology/feature-requests/43

Removed as this concept does not appear to be useful. Secretion is a process that may be defective in disease but does not appear to be a valid grouping term. For instance, insulin secretion may be defective in Diabetes melitis, but diabetes is not just a secretory disease.

Reported by: wakibbe

Original Ticket: diseaseontology/feature-requests/5

Hi,

I am writing to report a missing relation for Term ID: DOID_3125, Term
Name:multiple endocrine neoplasia, in the current version of the
ontology.

The OBO file was downloaded from
http://www.obofoundry.org/cgi-bin/detail.cgi?id=disease\_ontology
today, September 4th 2012. See attached screenshot in bioportal.

Thank you.

Reported by: *anonymous

Original Ticket: diseaseontology/feature-requests/31

I am attaching to the tracker an xls with the action taken for around 61 missing terms (mapping/creating). I am attaching also the temporary ontology file, where I have been mapping/adding terms with default ID ID:00000xx instead of DO:xxxx for better traceability.

I would like to receive your comments about the work, if it is welcome, if it is useful, and if you have suggestions or questions for the rest of the work that I would like to submit.

Best regards
Niccolo

Reported by: *anonymous

Original Ticket: diseaseontology/feature-requests/27

Lynn-turns out I don't have a second term request, but a request for synonyms to be added to the term Deafness dystonia syndrome. Thanks-Ranjana

Synonyms for Deafness Dystonia Sydrome (DOID:0050757):
Mohr-Tranebjaerg Syndrome
Dystonia Deafness Syndrome
Deafness Dystonia Optic Neuronopathy Syndrome (DDON)
Deafness Dystonia Optic Atrophy Syndrome

http://omim.org/entry/304700
http://www.ncbi.nlm.nih.gov/books/NBK1216/
http://ghr.nlm.nih.gov/condition/deafness-dystonia-optic-neuronopathy-syndrome

Reported by: ranjana

Original Ticket: diseaseontology/feature-requests/41

Removed as this concept does not appear to be useful and is subsumed by disease of material anatomical entity (DOID:5)

Reported by: wakibbe

Original Ticket: diseaseontology/feature-requests/6

Patent ductus arteriosus

http://www.nhlbi.nih.gov/health/dci/Diseases/pda/pda\_what.html

Reported by: wakibbe

Original Ticket: diseaseontology/feature-requests/15

C0011175 Dehydration should be obsoleted

Reported by: wakibbe

Original Ticket: diseaseontology/feature-requests/17

dm8qGS <a href="http://jjcozmzhczxw.com/"&gt;jjcozmzhczxw&lt;/a>, [url=http://mnocpsbvpwru.com/]mnocpsbvpwru[/url], [link=http://wgcivxtzefpo.com/]wgcivxtzefpo[/link], http://unghbpbgkzcz.com/

Reported by: *anonymous

Original Ticket: diseaseontology/feature-requests/34

see attachment.

Reported by: cmungall

Original Ticket: diseaseontology/feature-requests/9

synonym: FXTAS
OMIM:300623
is_a: neurodegenerative disease

PMID: 18195136 explains how this disease is distinct from fragile X syndrome (DOID:14261) even though the same gene is affected in both diseases. It would also be good to add an definition to DOID:14261.

Reported by: stweedie

Original Ticket: diseaseontology/feature-requests/46

The NCBI disease corpus can be downloaded here:
http://www.ncbi.nlm.nih.gov/CBBresearch/Fellows/Dogan/corpus.html

Any span with category = DiseaseClass or SpecificDisease should match to a primary DO label or to a synonym. (synonymous could even be annoted with the PMID).

This pipeline could be run regularly in Jenkins to check the completeness of DO over time.

Reported by: cmungall

Original Ticket: diseaseontology/feature-requests/38

We'd like a new term that corresponds to OMIM:614559

name: infantile cerebellar-retinal degeneration
synonyms: ICRD (from OMIM)
mitochondrial aconitase deficiency (from PMID:23438437)
OMIM:614559
is_a: neurodegenerative disease or central nervous system hereditary degenerative disease?
PMID:22405087 (ref for disease)
PMID:23438437 (describes the Drosophila model)

Thanks,
Susan

Reported by: stweedie

Original Ticket: diseaseontology/feature-requests/49

this class serves no purpose

Reported by: cmungall

Original Ticket: diseaseontology/feature-requests/14

[Term]
id: DOID:2370
name: diabetic nephropathy
namespace: disease_ontology
is_obsolete: true
xref: ICD9CM:250.4
xref: MSH:D003928
xref: NCI:C84417
xref: SNOMEDCT_2010_1_31:127013003
xref: SNOMEDCT_2010_1_31:190338009
xref: SNOMEDCT_2010_1_31:197605007
xref: SNOMEDCT_2010_1_31:21858001
xref: SNOMEDCT_2010_1_31:267470000
xref: SNOMEDCT_2010_1_31:54181000
xref: SNOMEDCT_2010_1_31:60009009
xref: UMLS_CUI:C0011881

consider:

* adding a reason for obsoletion in the comment field where possible

• adding consider or replaced_by field, pointing either to DO ID or term from other ontology (e.g. HP if the term was actually a phenotype)

Reported by: cmungall

Original Ticket: diseaseontology/feature-requests/32

I think the current definition of neurodegenerative disease; DOID:1289 (A central nervous system disease that results_in the progressive deterioration of tissue or organ function or structure, whether due to normal bodily wear or lifestyle choices.) should be expanded to reflect the fact that many of the diseases listed in this branch of the ontology are genetic disorders and not simply the result of wear or lifestyle choices. Alternatively, the last part of the definition could be removed.

Thanks,
Susan

Reported by: stweedie

Original Ticket: diseaseontology/feature-requests/47

[Diseaseontology-discussion] Colorectal Cancer, Liver Cancer, DO-slim?
Delete From: <peili_zhang@vr…> – 2008-05-20 15:17

1: why is ‘Colorectal Cancer’ (DOID:9256) NOT a
child (or grandchild..) of ‘digestive system cancer’ (DOID:8377)?

2: Why are the different stages of ‘Colorectal Cancer’ (stages I through IV) NOT even
linked to ‘Colorectal Cancer’ directly at all?

Peili Zhang, Ph.D.
Vertex Pharmaceuticals, Inc.
130 Waverly Street
Cambridge, MA 02139
617-444-6593

Reported by: lschriml

Original Ticket: diseaseontology/feature-requests/1

name: west nile virus neurological syndrome
def: "West nile virus neurological syndrome is a organic brain syndrome resulting from West Nile virus infection that may result in meningitis, encephalitis, acute laccid paralysis, Parkingsonian-like conditions or movement disorder." [URL:http://www.phac-aspc.gc.ca/wnv-vwn/hmncasedef-eng.php]
synonym: "West nile neuroinvasive disease" EXACT []
synonym: "WNND" EXACT []
synonym: "WNNS" EXACT []
is_a: DOID:225 ! syndrome

The genus of the definition mentions 'organic brain syndrome' (presumably DOID:777) but the is_a parent is 'syndrome'

Reported by: cmungall

Original Ticket: diseaseontology/feature-requests/13

MESH: http://www.nlm.nih.gov/cgi/mesh/2011/MB\_cgi?mode=&term=Rotavirus+Infections&field=entry

Infection with any of the rotaviruses. Specific infections include human infantile diarrhea, neonatal calf diarrhea, and epidemic diarrhea of infant mice.

Reported by: lindenb

Original Ticket: diseaseontology/feature-requests/28

Currently DO has the general sounding term myotonic dystrophy; DOID:11722 associated with dbxrefs to both OMIM:602668 (MYOTONIC DYSTROPHY 2; DM2) and OMIM:160900 (MYOTONIC DYSTROPHY 1; DM1). DOID:11722 has no definition at present but the links to both OMIM diseases imply it is a grouping term for the myotonic dystrophies. However that isn't compatible with the fact that DOID:11722 also has a single child term myotonic dystrophy type 2 ; DOID:0050759 (undefined and with no dbxrefs). It seems odd to have a single child when there are 2 types of DM and it looks like OMIM:602668 should be attached to DOID:0050759.

From a quick reading of the OMIM pages there appears to be a common set of clinical features for DM1 and DM2 but the underlying cause is a different gene in each case. Depending on whether you want to class DM1 and DM2 as distinct diseases or not, it would make sense to either:

A. Add a the new term 'myotonic dystrophy type 1' as new child of myotonic dystrophy DOID:11722 and migrate the OMIM IDs (and other dbxrefs) from DOID:11722 to the appropriate children.

or

B. Delete DOID:0050759 myotonic dystrophy type 2

Reported by: stweedie

Original Ticket: diseaseontology/feature-requests/48

We require the following terms for subtypes of breast cancer at the University of Arkansas for Medical Sciences.

estrogen-receptor positive breast cancer
estrogen-receptor negative breast cancer
progesterone-receptor positive breast cancer
progesterone-receptor negative breast cancer
Her2-receptor positive breast cancer
Her2-receptor negative breast cancer
Triple-receptor negative breast cancer

Her2 stands for Human Epidermal growth factor Receptor 2.
Triple negative means that it is all of ER negative, PR negative and Her2 negative.

Reported by: hoganwr

Original Ticket: diseaseontology/feature-requests/21

C0013481 Ebstein's Anomaly

http://www.americanheart.org/presenter.jhtml?identifier=11075

Reported by: wakibbe

Original Ticket: diseaseontology/feature-requests/16

[Term]
id: DOID:3308
name: embryonal carcinoma
def: "An embryonal cancer that is a type of germ cell tumour that is located_in the ovaries and located_in the testes." [url:http://en.wikipedia.org/wiki/Embryonal_carcinoma]

The expression "located_in some ovary and located_in some testis" is unsatisfiable.

I think you mean to say that is located_in the ovaries OR located_in the testes."

Reported by: cmungall

Original Ticket: diseaseontology/feature-requests/23

These could be vetted and added as xrefs, or, preferably as inter-ontology relationships. Need to decide on relation, e.g. has_location or affects_site

Reported by: cmungall

Original Ticket: diseaseontology/feature-requests/10

is_a: DOID:1289 ! neurodegenerative disease
def: "A rare, inherited, neurological movement disorder characterized by an abnormal accumulation of iron in the brain and progressive degeneration of the nervous system. Symptoms, which vary greatly among patients and usually develop during childhood, may include slow writhing, distorting muscle contractions of the limbs, face, or trunk, choreoathetosis (involuntary, purposeless jerky muscle movements), muscle rigidity (uncontrolled tightness of the muscles), spasticity (sudden, involuntary muscle spasms), ataxia (inability to coordinate movements), confusion, disorientation, seizures, stupor, and dementia. Other less common symptoms may include painful muscle spasms, dysphasia (difficulty speaking), mental retardation, facial grimacing, dysarthria (poorly articulated speech), and visual impairment. " [http://www.ninds.nih.gov/disorders/nbia/nbia.htm]

Reported by: cmungall

Original Ticket: diseaseontology/feature-requests/33

Reproductive system cancer should not be a child of genitourinary system cancer, as these two "systems" overlap (one is not entirely a part or component of the other). Given the FMA, perhaps breast cancer should go under thoracic cancer also.

Reported by: hoganwr

Original Ticket: diseaseontology/feature-requests/22

id: DOID:12659 is a Term named “Recruitment”, perhaps change name to “Auditory Recruitment”

Reported by: *anonymous

Original Ticket: diseaseontology/feature-requests/7

Removed as this concept does not appear to be useful and is subsumed by “disease of hematopoietic system” DOID:74

Reported by: wakibbe

Original Ticket: diseaseontology/feature-requests/4

some of these will represent equivalence relations

others will be is_as

both these cases will derive from a lack of consensus about where and how to make the disease v phenotype partition. One solution is to treat the DO term as the disposition rather than the actualized quality

Others will represent genuine disease-phenotype relationships. E.g:

DOID:14330-Parkinson disease HP:0003470-paralysis

(although this particular example is simplifying a complex relationship..)

If vetted, perhaps these could simply treated as semantics-free xrefs until we decide what to do with them?

Reported by: cmungall

Original Ticket: diseaseontology/feature-requests/11

Hi Lynn-Hope all is well, I have two term requests, but will create different tickets, since I think we agreed to do it that way. Thanks, Ranjana.

Jensen syndrome
http://omim.org/entry/311150

Synonyms:
Opticoacoustic nerve atrophy with dementia (in some sites this seems to be the Name)
Syndrome of opticoacoustic nerve atrophy with dementia
Nerve deafness optic nerve atrophy, and dementia
http://rarediseases.info.nih.gov/gard/3046/jensen-syndrome/resources/1

PMID:7195649
PMID:3425626

Reported by: ranjana

Original Ticket: diseaseontology/feature-requests/40

The discussion, via email, has been whether the DO term " Alzheimer's disease: is this term/definition inclusive of 'early-onset Alzheimer's', or should there be a child term for this form ?

Emails:
Barry Smith:
Another problem is that, as far as I (as a true ignoramus) can
tell, some of the definitions seem to be medically inaccurate. E.g. the definition for Alzheimer's excludes Early Onset Alzheimers:

A dementia that results in progressive memory loss, impaired thinking, disorientation, and changes in personality and mood starting in
late middle age and leads in advanced cases to a profound decline in cognitive and physical functioning and is marked histologically
by the degeneration of brain neurons especially in the cerebral cortex and by the presence of neurofibrillary tangles and plaques
containing beta-amyloid. It is characterized by memory lapses, confusion, emotional instability and progressive loss of mental
ability.

Lynn:
-- As for the definition of Alzheimer's you mentioned:
The definition is written to be inclusive of the two forms of Alzheimer's (early-onset AD [onset before age 65] and late-onset AD), we did not create separate diseases for the two forms, but rather: one term.
We include in the definition: starting in late middle age

Chris:
You might also want to consider it a NTR for "early onset Alzheimer's" as a subclass (presumably, but IANA expert)

Reported by: lschriml

Original Ticket: diseaseontology/feature-requests/25

[Diseaseontology-discussion] Colorectal Cancer, Liver Cancer, DO-slim?
Delete From: <peili_zhang@vr…> – 2008-05-20 15:17

Is there a
cut-down version of the Disease Ontology, similar to GO slim?

Peili Zhang, Ph.D.
Vertex Pharmaceuticals, Inc.
130 Waverly Street
Cambridge, MA 02139
617-444-6593

Reported by: lschriml

Original Ticket: diseaseontology/feature-requests/3

There are many problems with this file.

It is full of mistakes such as
'pneumonic plague' = 'lung disease' and located_in some lung

Many classes share the same logical definition.

Perhaps this was caused by a problem in an oboedit beta?

I am attaching a list of problematic cases that could be found automatically. There may be many more that are not so obviously wrong.

Note you can run your test for yourself using obo-check-xps.pl
https://github.com/cmungall/obo-scripts

I also recommend releasing with oort, this will spot these problems too

Reported by: cmungall

Original Ticket: diseaseontology/feature-requests/24