UMLS concept ID mappig

[przemokraw]

First of all I would like to thank you for sharing this dataset. It's great!

I am facing the following problem:
I have a NER and entity linker that links genes to NCBI GeneID (eg. TP53 has GeneID 7157, see https://www.ncbi.nlm.nih.gov/gene/?term=tp53), drugs to ChEMBL id (eg. https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL189707/) and diseases to Disease Ontology ID (http://disease-ontology.org/). I need to link my entities to corresponding UMLS concept IDs in order to evaluate my NER. Disease Ontology has an API that returns CUI for given DOID. Unfortunately, I don't know how to deal with genes and drugs. Please, give a hint if you know how to map NCBI GeneID or ChEMBL id to UMLS concept ID in reliable way.

Thank you for your great work and any help!

[czi-sunil]

I have not mapped from these ontologies, but was able to use the information in the MRCONSO.RRF file (part of the UMLS release) to map between MeSH and UMLS ids.

[sandertan]

Old thread, but perhaps this could help:

UMLS contains the HGNC gene dataset, so there is a mapping between CUI and GeneID. If you browse MRCONSO, you'll find the gene names and NCBI IDs and their respective UMLS CUI.

See:
https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/HGNC/stats.html
https://www.genenames.org/download/statistics-and-files/

[island99]

In the paper, it says:

entity descriptions (which in our case is the canonical name, the type, and a list of known aliases andsynonyms)

Is there any examples of entity descriptions to show? I'm not sure how to get the above and what they mean, thanks for the help.

[kaushikacharya]

Is there any examples of entity descriptions to show? I'm not sure how to get the above and what they mean, thanks for the help.

You can have a look at Metathesaurus Browser mentioned in https://www.nlm.nih.gov/research/umls/index.html
N.B. You would need to register first.

Here's an example screenshot:

Explanation:
Canonical Name: Nodule of lung

Aliases:

• pulmonary nodule
• lung nodule
  The above two are a subset of the aliases (mentioned under Atoms) for this entity.

[srishti-git1110]

Hi,
A very old thread, but I'm struggling to find a solution to a problem of mine and this thread looks very relevant. Please help me.

My question- I need to map some disease names (that I've tagged using a pre-trained tool) to MeSH+OMIM ontology as MeSH doesn't have genetic diseases, so any complete ontology for diseases shall use both MeSh + OMIM.

I have the CUIs corresponding to those diseases & would now like to map the CUI ids to MeSH+OMIM.

What are the possible solutions? Thanks in advance.

[czi-sunil]

UMLS contains mappings to source vocabularies. If you go to the UMLS Metathesaurus Browser and look up C5203670, which is the id for "COVID-19 (disease)", you will see a list of names from a bunch of source Vocabularies that are mapped to this concept. "MSH" is MeSH and "OMIM" is OMIM. This information is also in the MRCONSO.RRF file. *...............................Sunil Mohan* Research Scientist ***@***.*** http://chanzuckerberg.com <http://chanzuckerberg.com/?email>

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On Wed, May 4, 2022 at 12:05 PM srishti-git1110 ***@***.***> wrote: Hi, A very old thread, but I'm struggling to find a solution to a problem of mine and this thread looks very relevant. Please help me. My question- I need to map some disease names (that I've tagged using a pre-trained tool) to MeSH+OMIM ontology as MeSH doesn't have genetic diseases, so any complete ontology for diseases shall use both MeSh + OMIM. I have the CUIs corresponding to those diseases & would now like to map the CUI ids to MeSH+OMIM. What are the possible solutions? Thanks in advance. — Reply to this email directly, view it on GitHub <#5 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJY7ZHDQY7QDN2IXGN7AXDLVILC75ANCNFSM4IUFSYXA> . You are receiving this because you commented.Message ID: ***@***.***>

[srishti-git1110]

Thanks for answering.

I'll need to perform this mapping from cui to mesh+omim for quite a lot of data & need to integrate this into my code pipeline.
Do you have any idea how I could do this?

I tried to download the MRCONSO.RRF file (with a hope to accomplish my task using information from this file) but it requires some sort of license.

[czi-sunil]

Yes, you will need to get permission to download a UMLS release (I think you need to create an account, and describe your use). MRCONSO.RRF is part of the download. That is probably the best way to proceed. *...............................Sunil Mohan* Research Scientist ***@***.*** http://chanzuckerberg.com <http://chanzuckerberg.com/?email>

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On Thu, May 5, 2022 at 10:22 AM srishti-git1110 ***@***.***> wrote: Thanks for answering. I'll need to perform this mapping from cui to mesh+omim for quite a lot of data & need to integrate this into my code pipeline. Do you have any idea how I could do this? I tried to download the MRCONSO.RRF file (with a hope to accomplish my task using information from this file) but it requires some sort of license. — Reply to this email directly, view it on GitHub <#5 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJY7ZHEJMI67VHQYYCP4HK3VIP7VLANCNFSM4IUFSYXA> . You are receiving this because you commented.Message ID: ***@***.***>

[Youpu-Chen]

MedGen Database may be a manageable solution.

[Youpu-Chen]

MedGen Database may be a managable solution.