This CL adds a new import for NCBI Gene. The data cleaning and testin…

…g is documented on [GitHub](datacommonsorg/data#1084). NCBI Gene is updated daily. We included the following datasets in this import:

1. [NCBI Gene](https://ftp.ncbi.nih.gov/gene/DATA/gene_info.gz).
2. [gene2pubmed](https://ftp.ncbi.nih.gov/gene/DATA/gene2pubmed.gz).
3. [gene_neighbors](https://ftp.ncbi.nih.gov/gene/DATA/gene_neighbors.gz).
4. [gene_orthologs](https://ftp.ncbi.nih.gov/gene/DATA/gene_orthologs.gz).
5. [gene_group](https://ftp.ncbi.nih.gov/gene/DATA/gene_group.gz).
6. [mim2gene_medgen](https://ftp.ncbi.nih.gov/gene/DATA/mim2gene_medgen).
7. [gene2go](https://ftp.ncbi.nih.gov/gene/DATA/gene2go.gz).
8. [gene2accession](https://ftp.ncbi.nih.gov/gene/DATA/gene2accession.gz).
9. [gene2ensembl](https://ftp.ncbi.nih.gov/gene/DATA/gene2ensembl.gz).
10. [generifs_basic](https://ftp.ncbi.nih.gov/gene/GeneRIF/generifs_basic.gz).

[NCBI Gene](https://www.ncbi.nlm.nih.gov/gene) is a comprehensive resource containing information about genes from a wide range of species. It serves as a central hub for gene-specific data, integrating information from various sources and providing links to other relevant resources. It includes gene identification (e.g. official gene symbols, aliases, and cross-references to other databases), sequence information (e.g. genomic location and reference sequences (RefSeqs) for genomic DNA, transcripts, proteins, and mature peptides), functional information (gene function descriptions, associated pathways, related biological processes, orthologs, and related genes), phenotypic associations, (i.e. links to phenotypes and diseases associated with the gene), and links to relevant scientific papers (i.e. PubMed IDs).

"[NCBI Gene](https://www.ncbi.nlm.nih.gov/gene) supplies gene-specific connections in the nexus of map, sequence, expression, structure, function, citation, and homology data. Unique identifiers are assigned to genes with defining sequences, genes with known map positions, and genes inferred from phenotypic information. These gene identifiers are used throughout NCBI's databases and tracked through updates of annotation. Gene includes genomes represented by [NCBI Reference Sequences](https://www.ncbi.nlm.nih.gov/refseq/) (or RefSeqs) and is integrated for indexing and query and retrieval from NCBI's Entrez and [E-Utilities](https://www.ncbi.nlm.nih.gov/books/NBK25501/) systems. Gene comprises sequences from thousands of distinct taxonomic identifiers, ranging from viruses to bacteria to eukaryotes. It represents chromosomes, organelles, plasmids, viruses, transcripts, and millions of proteins."

PiperOrigin-RevId: 690868739

biomedical_schema/chemical_compound.mcf

@@ -21,7 +21,7 @@ description: "An antibody is a kind of protective protein which is produced by t
 Node: dcid:BiomedicalEntity
 name: "BiomedicalEntity"
 typeOf: schema:Class
-subClassOf: schema:BioChemEntity
+subClassOf: dcs:Thing
 description: "Biomedical related entities."
 
 Node: dcid:ChemicalCompound
@@ -546,20 +546,6 @@ rangeIncludes: schema:Boolean
 description: "The Clinical Pharmacogenetics Implementation Consortium (CPIC) was established in 2009 as a shared project between PharmGKB and the Pharmacogenomics Research Network (PGRN). CPIC is funded by the NIH/NHGRI. This indicates whether a gene has a drug dosing guideline issued by the CPIC that is associated with it."
 descriptionUrl: "https://www.pharmgkb.org/page/cpic"
 
-Node: dcid:hasGenomicCoordinates
-name: "hasGenomicCoordinates"
-typeOf: schema:Property
-domainIncludes: dcs:GenomeAnnotation
-rangeIncludes: dcs:GenomicCoordinates
-description: "Genomic coordinates specify the location of the position of an element within a specified genome assembly. It is a specified set of chromosome start_position end_position."
-
-Node: dcid:hasGeneticVariantAnnotation
-name: "hasGeneticVariantAnnotation"
-typeOf: schema:Property
-domainIncludes: dcs:Gene
-rangeIncludes: schema:Boolean
-description: "Indicates whether there are gene has genetic variants that are associated with it."
-
 Node: dcid:humanCellType
 typeOf: schema:Property
 name: "humanCellType"

biomedical_schema/disease.mcf

@@ -258,6 +258,15 @@ domainIncludes: dcs:MeSHConcept
 rangeIncludes: dcs:MeSHConcept
 description: "The preferred MeSH Concept to which the MeSH Concept that is narrower in scope is related."
 
+Node: dcid:ScopeNote
+name: "ScopeNote"
+typeOf: schema:Property
+rangeIncludes: schema:Text
+domainIncludes: dcs:Thing
+specializationOf: dcs:definition
+description: "A scope note is a concise explanatory text that defines the intended meaning and usage of a term or concept within a specific context. It clarifies the meaning of the term, specifies the boundaries of the concept, and provides guidance on its usage."
+descriptionUrl: "https://www.nlm.nih.gov/mesh/xml_data_elements.html#ScopeNote"
+
 Node: dcid:snomedCT
 typeOf: schema:Property
 name: "snomedCT"
@@ -269,12 +278,11 @@ descriptionUrl: "https://www.snomed.org/use-snomed-ct"
 Node: dcid:umlsConceptUniqueID
 typeOf: schema:Property
 name: "umlsConceptUniqueID"
-domainIncludes: dcs:Disease
-rangeIncludes: schema:Text,dcs:MeSHConcept
-description: "A Unified Medical Language System (UMLS) Concept Unique ID (CUI) is a unique identifier in the Metathesaurus for a concept. CUI contain the letter C followed by seven numbers. An example of a CUI is C0018681."
+domainIncludes: dcs:Disease, dcs:UmlsConceptUniqueIdentifier
+rangeIncludes: dcs:MeSHConcept, dcs:UmlsConceptUniqueIdentifier, schema:Text
+abbreviation: "CUI"
+description: "A concept is a meaning. A meaning can have many different names. A key goal of Metathesaurus construction is to understand the intended meaning of each name in each source vocabulary and to link all the names from all of the source vocabularies that mean the same thing (the synonyms). CUI contain the letter C followed by seven numbers. In the example on the right the CUI is C0018681."
 descriptionUrl: "https://www.nlm.nih.gov/research/umls/new_users/online_learning/Meta_005.html"
-synonym: "unified medical language system concept ID"
-sameAs: dcs:unifiedMedicalLanguageSystemConceptUniqueIdentifier
 
 Node: dcid:unifiedMedicalLanguageSystemConceptUniqueIdentifier
 typeOf: schema:Property