Linking proteins and humangenes annotation preferred name to identifier

[ibarshai]

I'm looking at annotations in the proteins and humangenes domain in the google_patent_research.annotations table. It appears that the annotations themselves are normalized to their preferred name, but I was wondering if there is any way to link the preferred name of the gene annotation to some kind of unique identifier, such as HGNC, that can be used to ground these annotations?

I see that there is huge amount of information in the ebi_chembl section, with seemingly promising table names, but haven't spotted a useful connection by looking through the schemas.

[wetherbeei]

You can link via the OCID to tables in sciwalker-open-data.data:ontologies_2020r02 tables - @c-ruttkies may be able to help join from there to another identifier.

[dhimmel]

Thanks @wetherbeei for the assistance!

sciwalker-open-data:ontologies_2020r02:human_genes_preflabel looks promising in that it maps preferred labels to OCID identifiers:

Row	ocid	name	date
1	102100007495	AR	2021-02-13
2	102100018113	C2	2021-02-13
3	102100012590	C3	2021-02-13
4	102100007517	C5	2021-02-13
5	102100007690	C6	2021-02-13

However, I am not sure what is an OCID and who mints them. But I think they are "Ontology Concept Identifiers" minted by SciWalker since https://bioregistry.io/ocid:102100007495 redirects to https://www.sciwalker.com/sciwalker/faces/ociddata.xhtml?ocid=102100007495.

Any advice @c-ruttkies on how to map OCID to other gene nomenclatures, such as ncbigene, ensembl, HGNC, etcetera would be much appreciated!

[wetherbeei]

The OntoChem team has added this table to map between OCIDs and other databases: sciwalker-open-data:ontologies_2020r02.ocid_xref

SELECT DISTINCT database FROM sciwalker-open-data.ontologies_2020r02.ocid_xref

1 | RefSeq |   2 | PDBeChem |   3 | MACROCYCL |   4 | OMIM |   5 | ORDO |   6 | ICD-O |   7 | ICD9CM_2006 |   8 | EPPO |   9 | physiology |   10 | GO |   11 | FEMA |   12 | NCI2004_11_17 |   13 | event |   14 | OC_REGIONS |   15 | InterPro |   16 | TC |   17 | HMDB |   18 | SUBMITTER |   19 | sn |   20 | ICD10CM |   21 | species |   22 | Beilstein |   23 | NCBITaxon |   24 | OrganicChemistryPortal |   25 | PMID |   26 | ChEMBL |   27 | UM-BBD_enzymeID |   28 | GARD |   29 | MESH |   30 | stedman |   31 | GC_ID |   32 | chemistry |   33 | Uniprot |   34 | GeneTree |   35 | DRUGBANK |   36 | Reactome |   37 | ICD-10 |   38 | KEGG |   39 | GeneID |   40 | GOC |   41 | MetaCyc |   42 | PubChem |   43 | SABIO-RK |   44 | Wikipedia |   45 | CiteXplore |   46 | OCID |   47 | EFO |   48 | tui |   49 | UMLS_CUI |   50 | EC |   51 | UM-BBD_reactionID |   52 | PermId |   53 | ls |   54 | CHEBI |   55 | RESID |   56 | NCI |   57 | SNOMECT |   58 | ChemIDplus |   59 | RHEA |   60 | ENMBRS |   61 | WIKICHEM |   62 | MTH |   63 | Reaxys |   64 | SNOMEDCT_US_2018_03_01 |   65 | SNOMEDCT_US_2019_03_01 |   66 | MeSH |   67 | UniPathway |   68 | DO |   69 | DERMO |   70 | ICD9CM |   71 | CSP2005 |   72 | SNOMEDCT_US_2018_09_01 |   73 | PDB |   74 | HGNC |   75 | Ensembl |   76 | WIKIDRUGS |   77 | JA |   78 | MTHICD9_2006 |   79 | Alan Wood's Pesticides |   80 | SNOMED_CT_US_2018_03_01 |   81 | anatomy |   82 | relations |

[dhimmel]

Thanks @wetherbeei and @c-ruttkies!

Here's a query showing which external databases human_genes_preflabel maps to via the ocids:

SELECT
  database, COUNT(*) AS n_mappings
FROM
  `sciwalker-open-data.ontologies_2020r02.human_genes_preflabel` AS human_genes_preflabel
INNER JOIN
  `sciwalker-open-data.ontologies_2020r02.ocid_xref` AS ocid_xref
ON
  human_genes_preflabel.ocid = ocid_xref.ocid
GROUP BY database
ORDER BY n_mappings DESC

Great to see so many external vocabularies, particularly Ensembl, GeneID, HGNC.

Row	database	n_mappings
1	Uniprot	225032
2	InterPro	87289
3	Ensembl	68954
4	PDB	60276
5	RefSeq	55689
6	GO	28481
7	HGNC	20319
8	KEGG	19431
9	GeneID	19174
10	GeneTree	18969
11	Reactome	18491
12	EC	6039
13	MetaCyc	1187
14	RHEA	628
15	UM-BBD_reactionID	33
16	Wikipedia	32
17	UM-BBD_enzymeID	16
18	RESID	9
19	TC	5
20	GOC	1

@ibarshai did you want to go ahead and close this issue unless we have any other questions?

[dhimmel]

And here is an example query to map gene preferred labels to ensembl gene IDs that returns 21362 results:

SELECT
  DISTINCT human_genes_preflabel.name AS gene_preflabel,
  ocid_xref.database_id AS ensembl_id
FROM
  `sciwalker-open-data.ontologies_2020r02.human_genes_preflabel` AS human_genes_preflabel
INNER JOIN
  `sciwalker-open-data.ontologies_2020r02.ocid_xref` AS ocid_xref
USING
  (ocid)
WHERE
  ocid_xref.database = "Ensembl"
  # exclude ensembl protein mappings
  AND ocid_xref.database_id LIKE "ENSG%"
ORDER BY
  gene_preflabel,
  ensembl_id

Row	gene_preflabel	ensembl_id
1	A1BG	ENSG00000121410
2	A1CF	ENSG00000148584
3	A2M	ENSG00000175899
4	A2ML1	ENSG00000166535
5	A3GALT2	ENSG00000184389
6	A4GALT	ENSG00000128274

[dhimmel]

Note that to map to patent annotations, it's not necessary to go through sciwalker-open-data.ontologies_2020r02.human_genes_preflabel, since ocid is available in patents-public-data.google_patents_research.annotations:

SELECT
  DISTINCT ocid_xref.database_id AS ensembl_gene_id,
  ocid,
  patent_annotations.preferred_name AS patent_annotation_preferred_name,
  human_genes_preflabel.name AS gene_preflabel,
  patent_annotations.publication_number,
  patent_annotations.domain,
  --   patent_annotations.source,
  --   patent_annotations.confidence,
  --   patent_annotations.character_offset_start,
  --   patent_annotations.character_offset_end
FROM
  `patents-public-data.google_patents_research.annotations` AS patent_annotations
INNER JOIN
  `sciwalker-open-data.ontologies_2020r02.ocid_xref` AS ocid_xref
USING
  (ocid)
LEFT JOIN
  `sciwalker-open-data.ontologies_2020r02.human_genes_preflabel` AS human_genes_preflabel
USING
  (ocid)
WHERE
  ocid_xref.database = "Ensembl"
  # exclude ensembl protein mappings
  AND ocid_xref.database_id LIKE "ENSG%"
  # restrict to single patent publication for development
  AND patent_annotations.publication_number = "JP-3820105-B2"
LIMIT
  1000

Row	ensembl_gene_id	ocid	patent_annotation_preferred_name	gene_preflabel	publication_number	domain
1	ENSG00000134853	102100004940	Platelet-derived growth factor receptor alpha	PDGFRA	JP-3820105-B2	humangenes
2	ENSG00000111537	102100016020	Interferon gamma	IFNG	JP-3820105-B2	humangenes
3	ENSG00000115008	102100018955	Interleukin-1 alpha	IL1A	JP-3820105-B2	humangenes
4	ENSG00000130427	101000292394	human Erythropoietin	null	JP-3820105-B2	proteins
5	ENSG00000174059	102100016492	Hematopoietic progenitor cell antigen CD34	CD34	JP-3820105-B2	humangenes
6	ENSG00000025708	102100008604	Thymidine phosphorylase	TYMP	JP-3820105-B2	humangenes
7	ENSG00000138798	102100010813	Pro-epidermal growth factor	EGF	JP-3820105-B2	humangenes
8	ENSG00000102265	102100002607	Erythroid-potentiating activity	TIMP1	JP-3820105-B2	humangenes
9	ENSG00000214274	102100018024	Angiogenin	ANG	JP-3820105-B2	humangenes
10	ENSG00000134531	102100010285	Epithelial membrane protein 1	EMP1	JP-3820105-B2	humangenes
11	ENSG00000109270	101000411504	human Ragulator complex protein LAMTOR3	null	JP-3820105-B2	proteins

[ravwojdyla]

👋 @wetherbeei noticed the 2022 release of the "ontologies" at sciwalker-open-data:ontologies_2022r01, would it be possible to publish ocid_xref for 2022 as well please?

[ravwojdyla]

Also ping @c-ruttkies, would appreciate your help as well please ^

[ravwojdyla]

FYI ocid_xref for 2022 was published, thanks OntoChem/Sciwalker. This issue can probably be closed btw.