check that these diseases are in our KG

[saramsey]

amyotrophic lateral sclerosis
Schimke immuno-osseous dysplasia
Spinocerebellar ataxia with neuropathy type 1
Fanconi Anemia
asthma
a disorder of sterol metabolism regulating behavior and neural development
infertility
endometrial cancer
lung cancer
Primary Ciliary Dyskinesia
premature birth
congenital heart disease
LCHAD deficiency
VLCAD deficiency
hepatoxicity
Deficiency of N-glycanase 1

[finnagin]

So, if these are the exact strings that should be in the node name I checked using the following cypher command on the rtxsteve container on rtxdev.saramsey.org:

match(n) where n.name in ["amyotrophic lateral sclerosis","Schimke immuno-osseous dysplasia","Spinocerebellar ataxia with neuropathy type 1","Fanconi Anemia","asthma","a disorder of sterol metabolism regulating behavior and neural development","infertility","endometrial cancer","lung cancer","Primary Ciliary Dyskinesia","premature birth","congenital heart disease","LCHAD deficiency","VLCAD deficiency","hepatoxicity","Deficiency of N-glycanase 1"] return n.name, n.id limit 50;

This returned the following 5 results:

n.name	n.id
"infertility"	"DOID:5223"
"congenital heart disease"	"DOID:1682"
"endometrial cancer"	"DOID:1380"
"asthma"	"DOID:2841"
"amyotrophic lateral sclerosis"	"DOID:332"

[dkoslicki]

A few more (using ParseQuestion.py):

disease	id
amyotrophic lateral sclerosis	DOID:332
Fanconi anemia	DOID:13636
asthma	DOID:2841
infertility	DOID:5223
endometrial cancer	DOID:1380
lung cancer	OMIM:211980
Primary Ciliary Dyskinesia	DOID:9562
premature birth	HP:0001622
congenital heart disease	DOID:1682

So it looks like we need:

• Schimke immuno-osseous dysplasia
• Spinocerebellar ataxia with neuropathy type 1
• a disorder of sterol metabolism regulating behavior and neural development
• LCHAD deficiency
• VLCAD deficiency
• hepatoxicity
• Deficiency of N-glycanase 1

[saramsey]

thanks @dkoslicki and also I agree with the priority label

[saramsey]

@finnagin can you please get DOIDs for these diseases, by manually searching in Monarch or in disease-ontology.org or in EBI OLS?

• Schimke immuno-osseous dysplasia
• Spinocerebellar ataxia with neuropathy type 1
• a disorder of sterol metabolism regulating behavior and neural development
• LCHAD deficiency
• VLCAD deficiency
• hepatoxicity
• Deficiency of N-glycanase 1

if you post the DOIDs here I will add them to seed_nodes.tsv

[finnagin]

Sure!

Our name	Name from source	ID
Schimke immuno-osseous dysplasia	Schimke immuno-osseous dysplasia	DOID:0060490
Spinocerebellar ataxia with neuropathy type 1	spinocerebellar ataxia type 1 with axonal neuropathy	DOID:0090115
a disorder of sterol metabolism regulating behavior and neural development	TBD	TBD
LCHAD deficiency	long chain 3-hydroxyacyl-CoA dehydrogenase deficiency	OMIM:609016
VLCAD deficiency	very long chain acyl-CoA dehydrogenase deficiency	DOID:0080155
hepatoxicity	TBD	TBD
Deficiency of N-glycanase 1	NGLY1-deficiency	DOID:0060728

[finnagin]

@saramsey Here are the disorders I mentioned in my email:

Name	ID
Desmosterolosis	OMIM:602398
CK syndrome	OMIM:300831
CHILD syndrome	OMIM:308050

[finnagin]

Here are the remaining sterol metabolism disorders (that have DOID/OMIM ids) I mentioned:

Name	ID
Greenberg dysplasia	OMIM:215140
Lathosterolosis	OMIM:607330
MEND syndrome	OMIM:300960
Smith-Lemli-Opitz syndrome	DOID:14692
X-linked chondrodysplasia punctata	DOID:0060292
mevalonic aciduria	DOID:0050452
Hyperimmunoglobulinemia d with periodic fever	OMIM:260920
cerebrotendinous xanthomatosis	DOID:4810
microcephaly-congenital cataract-psoriasiform dermatitis syndrome	OMIM:616834

[saramsey]

@DeqingQu can you please add these diseases to seed_nodes.tsv ? File has a simple TSV format with Unix line termination. Thank you.

[DeqingQu]

Done!

[saramsey]

verified all of these (except the "TBD" items) are in seed_nodes.tsv

[dkoslicki]

@jlmcclelland The bioentities in these comments should be relevant for your investigations.