README: Gene Last modified: January 2, 2025
NOTE: As files are added or modified in this ftp site, notification will be
sent via the Gene News RSS feed.
You may subscribe to the Gene News RSS feed here:
https://www.ncbi.nlm.nih.gov/feed/rss.cgi?ChanKey=genenews
A comparison of the files previously available from LocusLink to those now
available from Entrez Gene is provided here:
https://www.ncbi.nlm.nih.gov/entrez/query/static/help/LL2G.html#files
Files are provided in several directories and subdirectories.
This document is comprehensive, and subdivided according to the path in
which files are found.
Most of the files in this path are re-calculated daily. Gene does not,
however, compare previous and current data, so the date on the file may
change without any change in content.
Changes not affecting use of the ftp site:
15 Dec 2009: removed references to LocusLink
altered the labels in the interactions section, by appending 1
and 2
I. DATA directory
II. DATA directory, ASN_BINARY subdirectory
III. DATA directory, GENE_INFO subdirectory
IV. DATA directory, expression subdirectory
V. GeneRIF directory (includes reports of interactions)
VI. tools directory
VII. gene-related files from genome annotation
===========================================================================
===========================================================================
I. Files in the DATA directory
===========================================================================
===========================================================================
gene2accession recalculated daily
---------------------------------------------------------------------------
This file is a comprehensive report of the accessions that are
related to a GeneID. It includes sequences from the international
sequence collaboration, Swiss-Prot, and RefSeq. The RefSeq subset
of this file is also available as gene2refseq.
Because this file is updated daily, the RefSeq subset does not
reflect any RefSeq release. Versions of RefSeq RNA and protein
records may be more recent than those included in an annotation
release (build) or those in the current RefSeq release.
More notes about this file:
tab-delimited
one line per genomic/RNA/protein set of sequence accessions
Column header line is the first line in the file.
NOTE: Because this file is comprehensive, it may include
some RefSeq accessions that are not current, because they are
part of the annotation of the current genomic assembly. In other
words, the annotation of a genome is not continuous, but depends
on a data freeze. Sub-genomic RefSeqs, however, are updated
continuously. Thus some RefSeqs may have been replaced or
suppressed after a data freeze assocated with a genomic annotation.
Until the release of a new genomic annotation, all
RefSeqs that are included in the current annotation are reported
in this file.
---------------------------------------------------------------------------
tax_id:
the unique identifier provided by NCBI Taxonomy
for the species or strain/isolate
GeneID:
the unique identifier for a gene
status:
status of the RefSeq if a refseq, else '-'
RefSeq values are: INFERRED, MODEL, NA, PREDICTED, PROVISIONAL,
REVIEWED, SUPPRESSED, VALIDATED
RNA nucleotide accession.version:
may be null (-) for some genomes
RNA nucleotide gi:
the gi for an RNA nucleotide accession, '-' if not applicable
protein accession.version:
will be null (-) for RNA-coding genes
protein gi:
the gi for a protein accession, '-' if not applicable
genomic nucleotide accession.version:
may be null (-)
genomic nucleotide gi:
the gi for a genomic nucleotide accession, '-' if not applicable
start position on the genomic accession:
position of the gene feature on the genomic accession,
'-' if not applicable
position 0-based
NOTE: this file does not report the position of each exon.
For positions on RefSeq contigs and chromosomes,
use the gff3 file in the appropriate annotation directory.
For example, for the human genome,
ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/annotation_releases/
This file has one line for each feature.
WARNING: Positions in gff3 files are 1-based, not 0-based
NOTE: if genes are merged after an annotation is released, there
may be more than one location reported on a genomic sequence
per GeneID, each resulting from the annotation before the merge.
end position on the genomic accession:
position of the gene feature on the genomic accession,
'-' if not applicable
position 0-based
NOTE: this file does not report the position of each exon.
For positions on RefSeq contigs and chromosomes,
use the gff3 file in the appropriate annotation directory.
For example, for the human genome,
ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/annotation_releases/
This file has one line for each feature.
WARNING: Positions in gff3 files are 1-based, not 0-based
NOTE: if genes are merged after an annotation is released, there
may be more than one location reported on a genomic sequence
per GeneID, each resulting from the annotation before the merge.
orientation:
orientation of the gene feature on the genomic accession,
'?' if not applicable
assembly:
the name of the assembly
'-' if not applicable
mature peptide accession.version:
will be null (-) if absent
mature peptide gi:
the gi for a mature peptide accession, '-' if not applicable
Symbol:
the default symbol for the gene
===========================================================================
gene2ensembl recalculated daily
---------------------------------------------------------------------------
This file reports matches between NCBI and Ensembl annotation
based on comparison of rna and protein features.
Matches are collected as follows.
For a protein to be identified as a match between RefSeq and
Ensembl, there must be at least 80% overlap between the two.
Furthermore, splice site matches must meet certain conditions:
either 60% or more of the splice sites must match, or there may
be at most one splice site mismatch.
For rna features, the best match between RefSeq and Ensembl is
selected based on splice site and overlap comparisons. For coding
transcripts, there is no minimum threshold for reporting other than
the protein comparison criteria above. For non-coding transcripts,
the splice site criteria are the same as for protein matching, but
the overlap threshold is reduced to 50%.
Furthermore, both the rna and the protein features must meet these
minimum matching criteria to be considered a good match. In
addition, only the best matches will be reported in this file.
Other matches that satisified the matching criteria but were
not the best matches will not be reported in this file.
A summary report of species that have been compared is contained
in another FTP file, README_ensembl (see below).
Ensembl gene identifiers are also reported in the dbXrefs column
in the gene_info FTP file. Due to differences in how these files
are processed, the Ensembl gene identifiers in these two files
may not be in complete concordance.
More notes about this file:
tab-delimited
one line per match between RefSeq and Ensembl rna/protein
Column header line is the first line in the file.
---------------------------------------------------------------------------
tax_id:
the unique identifier provided by NCBI Taxonomy
for the species or strain/isolate
GeneID:
the unique identifier for a gene
Ensembl_gene_identifier:
the matching Ensembl identifier for the gene
RNA nucleotide accession.version:
the identifier for the matching RefSeq rna
will be null (-) if only the protein matched
Ensembl_rna_identifier:
the identifier for the matching Ensembl rna
may include a version number
will be null (-) if only the protein matched
protein accession.version:
the identifier for the matching RefSeq protein
will be null (-) if only the mRNA matched
Ensembl_protein_identifier:
the identifier for the matching Ensembl protein
may include a version number
will be null (-) if only the mRNA matched
===========================================================================
gene2vega archived
---------------------------------------------------------------------------
This file is no longer being updated. The last update was on
December 3, 2018.
This file reports matches between NCBI and Vega annotation.
Matches are derived from the comparisons between NCBI and
Ensembl annotation (which are reported in the gene2ensembl FTP
file). That is, where there is a match between NCBI and
Ensembl annotation, and there is a correspondence between that
Ensembl annotation and Vega annotation, then the inferred
relationship between the NCBI and Vega annotations are reported
here.
More notes about this file:
tab-delimited
one line per match between RefSeq and Vega rna/protein
Column header line is the first line in the file.
---------------------------------------------------------------------------
tax_id:
the unique identifier provided by NCBI Taxonomy
for the species or strain/isolate
GeneID:
the unique identifier for a gene
Vega_gene_identifier:
the matching Vega identifier for the gene
RNA nucleotide accession.version:
the identifier for the matching RefSeq rna
will be null (-) if only the protein matched
Vega_rna_identifier:
the identifier for the matching Vega rna
may include a version number
will be null (-) if only the protein matched
protein accession.version:
the identifier for the matching RefSeq protein
will be null (-) if only the mRNA matched
Vega_protein_identifier:
the identifier for the matching Vega protein
may include a version number
will be null (-) if only the mRNA matched
===========================================================================
README_ensembl recalculated weekly
---------------------------------------------------------------------------
This file reports the overall status of comparison between
NCBI and Ensembl annotation. The detailed report is contained
in the gene2ensembl FTP file (see above).
More notes about this file:
tab-delimited
one line per species
Column header line is the first line in the file.
---------------------------------------------------------------------------
tax_id:
the unique identifier provided by NCBI Taxonomy
for the species or strain/isolate
ncbi_release:
the NCBI release number
ncbi_assembly:
the NCBI assembly name
ensembl_release:
the Ensembl release number, or "Rapid" followed by the genebuild
for a comparison with an Ensembl Rapid release
ensembl_assembly:
the Ensembl assembly name
date_compared:
the date when the comparison was performed, in YYYYMMDD format
===========================================================================
gene2go recalculated daily
---------------------------------------------------------------------------
This file reports the GO terms that have been associated
with Genes in Entrez Gene.
Gene ontology annotations are imported from external sources
by processing the gene_association files on the GO ftp site:
http://www.geneontology.org/GO.current.annotations.shtml
and comparing the DB_Object_ID to annotation in Gene,
as also reported in gene_info.gz. This process is limited to the
species listed in go_process.xml file.
For all other species, gene ontology terms are computed at the time
of annotation by running InterProScan
(https://interproscan-docs.readthedocs.io/en/latest/), including analyses
against PANTHER trees on all annotated proteins and collating the
results by GeneID. These data are also provided in the GAF (GO
Annotation File) format in Genomes FTP. For example, see:
ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/949/774/975/GCF_949774975.1_mLagAlb1.1/
Multiple gene_associations files may be used for any genome.
If so, duplicate information is not reported; but unique
contributions of GO terms, evidence codes, and citations are.
The file that is used to establish the rules for
the files and fields that are used for each taxon
is documented in go_process.xml
MODIFIED: May 9, 2006 to include the category of the GO term.
MODIFIED: May 21, 2007 to use '-' for empty fields.
Data elements which are not applicable are shown as '-'.
tab-delimited
One line per GeneID/GO term/representative GO evidence code.
Column header line is the first line in the file.
---------------------------------------------------------------------------
tax_id:
the unique identifier provided by NCBI Taxonomy
for the species or strain/isolate
GeneID:
the unique identifier for a gene
GO ID:
the GO ID, formatted as GO:0000000
Evidence:
the evidence code in the gene_association file
Qualifier:
a qualifier for the relationship between the gene
and the GO term
GO term:
the term indicated by the GO ID
PubMed:
pipe-delimited set of PubMed uids reported as evidence
for the association
Category:
the GO category (Function, Process, or Component)
===========================================================================
gene2pubmed recalculated daily
---------------------------------------------------------------------------
This file can be considered as the logical equivalent of
what is reported as Gene/PubMed Links visible in Gene's
and PubMed's Links menus. Although gene2pubmed is re-calculated daily,
some of the source documents (GeneRIFs, for example) are not
updated that frequently, so timing depends on the update
frequency of the data source.
Documentation about how these links are maintained
is provided here:
https://www.ncbi.nlm.nih.gov/entrez/query/static/entrezlinks.html#gene
tab-delimited
one line per set of tax_id/GeneID/PMID
Column header line is the first line in the file.
---------------------------------------------------------------------------
tax_id:
the unique identifier provided by NCBI Taxonomy
for the species or strain/isolate
GeneID:
the unique identifier for a gene
PubMed ID (PMID):
the unique identifier in PubMed for a citation
===========================================================================
gene2refseq recalculated daily
---------------------------------------------------------------------------
tab-delimited
one line per genomic/RNA/protein set of RefSeqs
Column header line is the first line in the file.
Because this file is updated daily, the RefSeq subset does not
reflect any RefSeq release. Versions of RefSeq RNA and protein
records may be more recent than those included in an annotation
release (build) or those in the current RefSeq release.
NOTE: Because this file is comprehensive, it may include
some RefSeq accessions that are not current, because they are
part of the annotation of the current genomic assembly. In other
words, the annotation of a genome is not continuous, but depends
on a data freeze. Sub-genomic RefSeqs, however, are updated
continuously. Thus some RefSeqs may have been replaced or
suppressed after a data freeze associated with a genomic annotation.
Until the release of a new genomic annotation, all
RefSeqs included in the current annotation are reported
in this file.
NOTE: This file is the RefSeq subset of gene2accession.
---------------------------------------------------------------------------
tax_id:
the unique identifier provided by NCBI Taxonomy
for the species or strain/isolate
GeneID:
the unique identifier for a gene
status:
status of the RefSeq
values are: INFERRED, MODEL, NA, PREDICTED, PROVISIONAL,
REVIEWED, SUPPRESSED, VALIDATED
RNA nucleotide accession.version:
may be null (-) for some genomes
RNA nucleotide gi:
the gi for an RNA nucleotide accession, '-' if not applicable
protein accession.version:
will be null (-) for RNA-coding genes
protein gi:
the gi for a protein accession, '-' if not applicable
genomic nucleotide accession.version:
may be null (-) if a RefSeq was provided after
the genomic accession was submitted
genomic nucleotide gi:
the gi for a genomic nucleotide accession, '-' if not applicable
start position on the genomic accession:
position of the gene feature on the genomic accession,
'-' if not applicable
position 0-based
NOTE: this file does not report the position of each exon.
For positions on RefSeq contigs and chromosomes,
use the gff3 file in the appropriate annotation directory.
For example, for the human genome,
ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/annotation_releases/
WARNING: positions in these files are 1-based, not 0-based
NOTE: if genes are merged after an annotation is released, there
may be more than one location reported on a genomic sequence
per GeneID, each resulting from the annotation before the merge.
end position on the genomic accession:
position of the gene feature on the genomic accession,
'-' if not applicable
position 0-based
NOTE: this file does not report the position of each exon.
For positions on RefSeq contigs and chromosomes,
use the gff3 file in the appropriate annotation directory.
For example, for the human genome,
ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/annotation_releases/
WARNING: positions in these files are 1-based, not 0-based
NOTE: if genes are merged after an annotation is released, there
may be more than one location reported on a genomic sequence
per GeneID, each resulting from the annotation before the merge.
orientation:
orientation of the gene feature on the genomic accession,
'?' if not applicable
assembly:
the name of the assembly
'-' if not applicable
mature peptide accession.version:
will be null (-) if absent
mature peptide gi:
the gi for a mature peptide accession, '-' if not applicable
Symbol:
the default symbol for the gene
===========================================================================
gene2sts archived
---------------------------------------------------------------------------
This file is no longer being updated. The last update was on
July 26, 2017.
tab-delimited
one line per GeneID, UniSTS ID pair
Column header line is the first line in the file.
---------------------------------------------------------------------------
GeneID:
the unique identifier for a gene
UniSTS ID:
the unique identifier given to a primer pair by UniSTS
===========================================================================
gene2unigene archived
---------------------------------------------------------------------------
This file is no longer being updated. The last update was on
June 19, 2019.
This file can be considered as the logical equivalent of
what is reported as Gene/UniGene Links visible in Gene's
and UniGene's Links menus.
Documentation about how these links are maintained
is provided here:
https://www.ncbi.nlm.nih.gov/entrez/query/static/entrezlinks.html
tab-delimited
Column header line is the first line in the file.
Note: tax_id is not provided in a separate column. The prefix
of the UniGene cluster can be used to determine
the species
---------------------------------------------------------------------------
GeneID:
the unique identifier for a gene
UniGene cluster:
===========================================================================
gene_group recalculated daily
---------------------------------------------------------------------------
report of genes and their relationships to other genes
tab-delimited
one line per pair of GeneIDs
Column header line is the first line in the file.
NOTE: This file is not comprehensive, and contains
a subset of information summarizing gene-gene relationships.
Relationships are reported symmetrically, where appropriate, and
currently include:
Ortholog*
Potential readthrough sibling
Readthrough child
Readthrough parent
Readthrough sibling
Region member
Region parent
Related functional gene
Related pseudogene
*Note that Ortholog records appear in the gene_orthologs
file, and are excluded from the gene_group file.
Note also that the gene_group and gene_orthologs files use the
same column format.
---------------------------------------------------------------------------
tax_id:
the unique identifier provided by NCBI Taxonomy
for the species or strain/isolate
GeneID:
the current unique identifier for a gene
relationship:
the type of relationship between the two genes,
e.g. GeneID has a 'relationship' to Other GeneID
Other tax_id:
the related gene's tax_id
Other GeneID:
the related gene's GeneID
===========================================================================
gene_orthologs recalculated daily
---------------------------------------------------------------------------
report of orthologous genes
tab-delimited
one line per pair of GeneIDs
Column header line is the first line in the file.
The column format is the same as the gene_group file. In this
file, the relationship column value is always "Ortholog".
Ortholog gene groups are calculated by NCBI's Eukaryotic Genome
Annotation Pipeline for the NCBI Gene dataset using a combination
of protein sequence similarity and local synteny information.
Orthologous gene relationships may additionally be assigned after
manual review by a RefSeq genome curator. Orthology is determined
between a genome being annotated and a reference genome—such as the
cat and human genomes, respectively. For instance, if a cat gene
is identified as an ortholog of a human gene, it is included in the
set of genes from various organisms recognized as orthologs to that
human gene. Consequently, the "ortholog set" for the human gene
may contain genes from multiple organisms that can be regarded as
one-to-one orthologs of each other. For a description of the NCBI
ortholog calculation procedure, see
https://www.ncbi.nlm.nih.gov/kis/info/how-are-orthologs-calculated/
This file does not report relationships symmetrically. Instead, a
primary organism/gene is identified for each ortholog, and is
represented in the first two columns. All other orthologous
organisms/genes are represented in the last two columns. Therefore,
each record in the file represents a pair of orthologous genes. If
there are N orthologous genes in a group, then there will be N-1
records (pairs) represented in the gene_orthologs file. For
example, a human gene ortholog set that includes mouse, rat, cat
and dog genes will be represented by the following 4 rows in the
gene_orthologs file: human::mouse, human::rat, human::cat, and
human::dog.
===========================================================================
gene_history recalculated daily
---------------------------------------------------------------------------
comprehensive information about GeneIDs that are no longer current
tab-delimited
one line per GeneID
Column header line is the first line in the file.
---------------------------------------------------------------------------
tax_id:
the unique identifier provided by NCBI Taxonomy
for the species or strain/isolate
GeneID:
the current unique identifier for a gene
Discontinued GeneID:
the GeneID that is no longer current
Discontinued Symbol:
the symbol that was assigned to the discontinued GeneID,
if the discontinued record was not replaced with another
Discontinue Date:
the date the gene record was discontinued or replaced, in
YYYYMMDD format
===========================================================================
gene_info recalculated daily
---------------------------------------------------------------------------
tab-delimited
one line per GeneID
Column header line is the first line in the file.
Note: subsets of gene_info are available in the DATA/GENE_INFO
directory (described later)
This file is identical in content to GENE_INFO/All_Data.gene_info.gz
even though their file sizes and timestamps may differ
slightly
---------------------------------------------------------------------------
tax_id:
the unique identifier provided by NCBI Taxonomy
for the species or strain/isolate
GeneID:
the unique identifier for a gene
ASN1: geneid
Symbol:
the default symbol for the gene
ASN1: gene->locus
LocusTag:
the LocusTag value
ASN1: gene->locus-tag
Synonyms:
bar-delimited set of unofficial symbols for the gene
dbXrefs:
bar-delimited set of identifiers in other databases
for this gene. The unit of the set is database:value.
Note that HGNC and MGI include 'HGNC' and 'MGI', respectively,
in the value part of their identifier. Consequently,
dbXrefs for these databases will appear like:
HGNC:HGNC:1100
This would be interpreted as database='HGNC', value='HGNC:1100'
Example for MGI:
MGI:MGI:104537
This would be interpreted as database='MGI', value='MGI:104537'
chromosome:
the chromosome on which this gene is placed.
for mitochondrial genomes, the value 'MT' is used.
map location:
the map location for this gene
description:
a descriptive name for this gene
type of gene:
the type assigned to the gene according to the list of options
provided in https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn
Symbol from nomenclature authority:
when not '-', indicates that this symbol is from a
a nomenclature authority
Full name from nomenclature authority:
when not '-', indicates that this full name is from a
a nomenclature authority
Nomenclature status:
when not '-', indicates the status of the name from the
nomenclature authority (O for official, I for interim)
Other designations:
pipe-delimited set of some alternate descriptions that
have been assigned to a GeneID
'-' indicates none is being reported.
Modification date:
the last date a gene record was updated, in YYYYMMDD format
Feature type:
pipe-delimited set of annotated features and their classes or
controlled vocabularies, displayed as feature_type:feature_class
or feature_type:controlled_vocabulary, when appropriate; derived
from select feature annotations on RefSeq(s) associated with the
GeneID
===========================================================================
gene_neighbors recalculated daily
---------------------------------------------------------------------------
This file reports neighboring genes for all genes placed on a
given genomic sequence.
More notes about this file:
tab-delimited
one line per GeneID and genomic placement
Column header line is the first line in the file.
genomic sequences in scope for reporting include all top-level
sequences and curated genomic (NG_ accessions)
---------------------------------------------------------------------------
tax_id:
the unique identifier provided by NCBI Taxonomy
for the species or strain/isolate
GeneID:
the unique identifier for a gene
genomic accession.version:
genomic gi:
the gi for a genomic nucleotide accession
start position:
start position of the gene feature on the genomic accession
position value is 0-based
end position:
end position of the gene feature on the genomic accession
position value is 0-based
orientation:
orientation of the gene feature on the genomic accession
chromosome:
the chromosome on which this gene is placed.
for mitochondrial genomes, the value 'MT' is used.
'-' if not applicable
GeneIDs on left:
bar-delimited set of GeneIDs for the nearest two non-overlapping
non-biological-region genes on the left, or '-' if there are none
additional GeneIDs may be included if the neighboring genes
overlap each other
distance to left:
distance to the nearest gene on the left, or '-' if there is none
GeneIDs on right:
bar-delimited set of GeneIDs for the nearest two non-overlapping
non-biological-region genes on the right, or '-' if there are none
additional GeneIDs may be included if the neighboring genes
overlap each other
distance to right:
distance to the nearest gene on the right, or '-' if there is none
overlapping GeneIDs:
bar-delimited set of GeneIDs for all overlapping genes,
or '-' if there are none
assembly:
the name of the assembly
'-' if not applicable
===========================================================================
gene_refseq_uniprotkb_collab recalculated every month
---------------------------------------------------------------------------
report of the relationship between NCBI Reference Sequence
protein accessions and UniProtKB protein accessions
tab-delimited
one line per pair
Column header line is the first line in the file.
The NCBI RefSeq::UniProt accession pairs represented in this file
are sourced, as indicated by the term in "method" column, in one of
the following ways:
1. "uniprot" -- NCBI RefSeq::UniProt matches imported from UniProt
2. "identical" -- NCBI RefSeq::UniProt matches where the protein
sequence and assigned organism of the two accessions are identical
to each other
3. "similar" -- NCBI RefSeq::UniProt matches where both of the
proteins have the same assigned organism and share >90% sequence
identity over >80% coverage
NCBI protein accession:
the protein accession of the RefSeq
UniProtKB protein accession:
the corresponding UniProtKB protein accession
NCBI_tax_id:
the unique identifier provided by NCBI Taxonomy for the species or
strain/isolate, for the NCBI protein accession
UniProtKB_tax_id:
the unique identifier provided by NCBI Taxonomy for the species or
strain/isolate, for the UniProtKB protein accession
method:
method by which the NCBI RefSeq::UniProt accession pair was
determined; see above for explanation
===========================================================================
gene_summary recalculated daily
---------------------------------------------------------------------------
extract of gene summary texts for live genes that have them
tab-delimited
one line per GeneID
Column header line is the first line in the file.
---------------------------------------------------------------------------
tax_id:
the unique identifier provided by NCBI Taxonomy
for the species or strain/isolate
GeneID:
the current unique identifier for a gene
Source:
the name of the source that provided the summary, for selected
sources
Summary:
the gene summary text
===========================================================================
go_process.xml
---------------------------------------------------------------------------
Rules for mapping information in the gene_info file
in this directory to the enumerated authority files
===========================================================================
mim2gene_medgen daily
---------------------------------------------------------------------------
report of the relationship between MIM numbers (OMIM),
GeneIDs, and Records in MedGen
tab-delimited
one line per MIM number
Column header line is the first line in the file.
Tax_id is not included because this file is relevant only for
human, tax_id 9606.
see also: http://omim.org/help/faq
In June, 2015, this file was modified to add a Comment column,
to qualify the relationship between a gene and a disorder as
reported by OMIM.
---------------------------------------------------------------------------
MIM number:
a MIM number associated with a GeneID
GeneID:
the current unique identifier for a gene
the lack of a GeneID, for whatever reason, is represented as a '-'
type:
type of relationship between the MIM number and the
GeneID
current values are
'gene' the MIM number associated with a Gene,
or a GeneID that is assigned to a record
where the molecular basis of the disease
is not known
'phenotype' the MIM number associated with a disease
that is associated with a gene
If NCBI has no record of this MIM number in its databases yet, there
is a '-' provided in the type column
source:
This value is provided only when there is a report of a relationship
between a MIM number that is a phenotype, and a GeneID.
The current expected values are GeneMap (from OMIM), GeneReviews,
and NCBI.
MedGenCUI:
The accession assigned by MedGen to this phenotype. If the accession starts
with a C followed by integers, the identifier is a concept ID (CUI) from UMLS.
https://www.nlm.nih.gov/research/umls/
If it starts with a CN, no CUI in UMLS was identified, and NCBI created
a placeholder.
Comment:
optional value reporting the qualifiers OMIM provides when reporting
a gene/phenotype relationship
The values are based on the explanation of the
symbols provided by OMIM: http://omim.org/help/faq
nondisease: Brackets, "[ ]", indicate "nondiseases,"
mainly genetic variations that lead to
apparently abnormal laboratory test values
(e.g., dysalbuminemic euthyroidal hyperthyroxinemia).
susceptibility: {} indicate mutations that contribute to
susceptibility to multifactorial disorders
QTL 1: {} and qtl
QTL 2: [] and qtl
somatic: somatic in the disease name
question: A question mark, "?", before the disease name
indicates an unconfirmed or possibly spurious mapping.
===========================================================================
stopwords_gene
---------------------------------------------------------------------------
A list of stopwords that are automatically excluded from
searches in Gene.
see also:
https://www.ncbi.nlm.nih.gov/books/NBK3841/#EntrezGene.Words_Excluded_From_Queries
===========================================================================
===========================================================================
II. Files in the DATA/ASN_BINARY directory
---------------------------------------------------------------------------
This directory and all its subdirectories contain complete extractions from
Entrez Gene in binary ASN.1 format, as Entrezgene sets.
These files are in binary ASN.1 format, and can readily be converted to XML
via the tool gene2xml documented below.
===========================================================================
===========================================================================
All_Data.ags.gz all records
Organelles.ags.gz Organelles only
Plasmids.ags.gz Plasmids only
Archea_Bacteria directory for Genes from Archaea and
Bacteria
All_Archaea_Bacteria.ags.gz all records from Archaea and Bacteria
Archaea.ags.gz Archaea only
Bacteria.ags.gz Bacteria only
Escherichia_coli_str._K-12_substr._MG1655.ags.gz
Escherichia coli K-12 MG1655 only
Pseudomonas_aeruginosa_PAO1.ags.gz
Pseudomonas aeruginosa PAO1 only
Fungi directory for Genes from Fungi
All_Fungi.ags.gz all records from Fungi, including
organelles
Ascomycota.ags.gz Ascomycota only
Microsporidia.ags.gz Microsporidia only
Penicillium_chrysogenum_Wisconsin_54-1255.ags.gz
Penicillium chrysogenum Wisconsin 54 only
Saccharomyces_cerevisiae.ags.gz
Saccharomyces cerevisiae only
Invertebrates directory for genes from invertebrates
All_Invertebrates.ags.gz all records from invertebrates
Anopheles_gambiae.ags.gz Anopheles gambiae only
Caenorhabditis_elegans.ags.gz Caenorhabditis elegans only
Drosophila_melanogaster.ags.gz Drosophila melanogaster only
Mammalia directory for genes from mammals
All_Mammalia.ags.gz all records from mammals, including
organelles
Bos_taurus.ags.gz Bos taurus only
Canis_familiaris.ags.gz Canis familiaris only
Homo_sapiens.ags.gz Homo sapiens only
Mus_musculus.ags.gz Mus musculus only
Pan_troglodytes.ags.gz Pan troglodytes only
Rattus_norvegicus.ags.gz Rattus norvegicus only
Sus_scrofa.ags.gz Sus scrofa only
Non-mammalian_vertebrates directory for non-mammalian vertebrates
All_Non-mammalian_vertebrates.ags.gz
all records from non-mammalian vertebrates
Danio_rerio.ags.gz Danio rerio only
Gallus_gallus.ags.gz Gallus gallus only
Xenopus_laevis.ags.gz Xenopus laevis only
Xenopus_tropicalis.ags.gz Xenopus tropicalis only
Plants directory for plants
All_Plants.ags.gz all records from plants
Arabidopsis_thaliana.ags.gz Arabidopsis thaliana only
Chlamydomonas_reinhardtii.ags.gz
Chlamydomonas reinhardtii only
Oryza_sativa.ags.gz Oryza sativa only
Zea_mays.ags.gz Zea mays only
Protozoa directory for protozoa
All_protozoa.ags.gz all records from protozoa
Plasmodium_falciparum.ags.gz Plasmodium falciparum only
Viruses directory for viruses
All_Viruses.ags.gz all records from viruses
Retroviridae.ags.gz Retroviridae only
===========================================================================
===========================================================================
III. Files in the DATA/GENE_INFO directory
---------------------------------------------------------------------------
This directory and all its subdirectories contain extractions from
Entrez Gene in the same format as the gene_info file (described earlier).
Each file contains a subset of data for the species or taxonomic group
indicated by the file name.
The content and directory structure mirror the content and structure of the
ASN_BINARY directory. The file names in this directory are qualified to
distinguish them from the binary ASN.1 files. For example, the gene_info
subset file for human will be found in:
DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz
The gene_info.gz file will continue to be updated in its original location
in the DATA directory.
The DATA/GENE_INFO/All_Data.gene_info.gz file is identical in content to
DATA/gene_info.gz even though their file sizes and timestamps may differ
slightly.
===========================================================================
===========================================================================
IV. Files in the DATA/expression directory
---------------------------------------------------------------------------
This directory and all its subdirectories contain reports of normalized RNA
expression levels computed from RNA-seq data for human, mouse, and rat
genes.
For details, see the README_expression contained therein.
===========================================================================
===========================================================================
V. Files in the GeneRIF directory (Gene References into Function)
===========================================================================
===========================================================================
generifs_basic.gz
---------------------------------------------------------------------------
GeneRIFs describing a single Gene each
(rather than interactions between two genes' products)
Tab-delimited
Sorted by Tax ID, Gene ID, and the first PubMed ID in the list
For more information, please review:
https://www.ncbi.nlm.nih.gov/gene/about-generif
---------------------------------------------------------------------------
Tax ID
the unique identifier provided by NCBI Taxonomy
for the species or strain/isolate
Gene ID
the unique identifier for a gene
PubMed ID (PMID) list
unique citation identifier(s) in PubMed;
multiple values are comma-separated
NOTE: if you process this by Excel, please be certain
to treat this column as a string. Otherwise comma-delimited
PubMed uids may be converted to a single integer
last update timestamp
the last time this GeneRIF was modified,
in ISO 8601 format "yyyy-mm-dd hh:mm"
GeneRIF text
GeneRIF text string, length <= 425 characters
===========================================================================
hiv_interactions.gz
---------------------------------------------------------------------------
Descriptions of interactions between two genes' products --
specifically, one from Human and one from Human Immunodeficiency
Virus type 1 (HIV-1) -- from a collaboration with NIAID
This file contains a subset of the interaction data reported in
interactions.gz, described below.
Tab-delimited
Sorted by: human Gene ID, human accession.version,
virus Gene ID, virus accession.version,
first PubMed ID in the list
---------------------------------------------------------------------------
First gene of interacting pair (virus interactant)
Tax ID 1
the unique identifier provided by NCBI Taxonomy
for the species or strain/isolate
Gene ID 1
the unique identifier for a gene
product accession.version 1
product name 1
Interaction short phrase
text string
Second gene of interacting pair (human interactant)
Tax ID 2
the unique identifier provided by NCBI Taxonomy
for the species or strain/isolate
Gene ID 2
the unique identifier for a gene
product accession.version 2
product name 2
PubMed ID (PMID) list
unique citation identifier(s) in PubMed;
multiple values are comma-separated
NOTE: if you process this by Excel, please be certain
to treat this column as a string. Otherwise comma-delimited
PubMed uids may be converted to a single integer
last update timestamp
the last time this GeneRIF was modified,
in ISO 8601 format "yyyy-mm-dd hh:mm"
GeneRIF text
text string, length <= 425 characters
===========================================================================
hiv_siRNA_interactions.gz
---------------------------------------------------------------------------
Descriptions of HIV-1 virus and human protein interactions that
regulate HIV-1 replication and infectivity.
All interactions are with Human immunodeficiency virus 1
(NC_001802.1, Tax ID 11676).
Tab-delimited
---------------------------------------------------------------------------
Tax ID
the unique identifier provided by NCBI Taxonomy
for the species or strain/isolate
Gene ID
the unique identifier for a gene
Interaction short phrase
text string
product accession.version
product name
PubMed ID (PMID) list
unique citation identifier(s) in PubMed;
multiple values are comma-separated
NOTE: if you process this by Excel, please be certain
to treat this column as a string. Otherwise comma-delimited
PubMed uids may be converted to a single integer
last update timestamp
the last time this GeneRIF was modified,
in ISO 8601 format "yyyy-mm-dd hh:mm"
GeneRIF text
text string, length <= 425 characters
===========================================================================
interactions.gz
---------------------------------------------------------------------------
Descriptions of interactions involving up to two interactants
and a resulting complex, at least one of which is a gene product.
If both interactants are associated with Gene IDs, the interacting
pair is reported once, using the convention that the interactant
with the smaller Gene ID is listed as the "first interactant",
as defined below.
This file includes the interaction data reported in
hiv_interactions.gz and hiv_siRNA_interactions.gz, described above.
Data elements which are not applicable are shown as "-".
Tab-delimited
Sorted by: 1st Tax ID, 1st Gene ID, 1st accession.version,
2nd Tax ID, 2nd accession.version,
first PubMed ID in the list
---------------------------------------------------------------------------
First interactant
Tax ID 1
the unique identifier provided by NCBI Taxonomy
for the species or strain/isolate
Gene ID 2
the unique identifier for a gene
interactant accession.version 1
interactant name 1
Interaction short phrase
text string
Second interactant
Tax ID 2
the unique identifier provided by NCBI Taxonomy
for the species or strain/isolate
interactant ID 2
an identifier for this interactant, within the database
specified by "interactant ID type" below
-- note: depending on the database, this ID may be
either a numeric value or a character string
interactant ID type
the database within which the interactant ID may be found;
if this interactant is a gene product, its interactant ID type
is "GeneID", and the interactant ID is its numeric Gene ID.
interactant accession.version 2
interactant name 2
Resulting complex
complex ID
an identifier for this complex, within the database
specified by "complex ID type" below
-- note: depending on the database, this ID may be
either a numeric value or a character string
complex ID type
the database within which the complex ID may be found
complex name
PubMed ID (PMID) list
unique citation identifier(s) in PubMed;
multiple values are comma-separated
NOTE: if you process this by Excel, please be certain
to treat this column as a string. Otherwise comma-delimited
PubMed uids may be converted to a single integer
last update timestamp
the last time this GeneRIF was modified,
in ISO 8601 format "yyyy-mm-dd hh:mm"
GeneRIF text
text string, length <= 425 characters
Interaction source
interaction ID
an identifier for this interaction, within the database
specified by "interaction ID type" below
-- note: depending on the database, this ID may be
either a numeric value or a character string
interaction ID type
the database within which the interaction ID may be found;
if there is no interaction ID, no interaction ID type is reported
additional information on interaction source databases is in
the file interaction_sources, described below.
===========================================================================
interaction_sources
---------------------------------------------------------------------------
Additional information on sources of interactions listed in
interactions.gz, described above.
Tag/value pairs, one per line, delimited by colon and whitespace
Sources delimited by blank lines
Sorted by symbol
---------------------------------------------------------------------------
Symbol
the symbol used to represent this source in interactions.gz
Webpage URL
the primary or general Web page for this source
Template URL
a prefix which, when combined with the interaction ID from a
specific interaction record in interactions.gz, produces a full
URL which accesses further information on that interaction from
the source's Web site
===========================================================================
===========================================================================
VI. Files in the Tools directory
===========================================================================
===========================================================================
i. taxidToGeneNames.pl
---------------------------------------------------------------------------
A representative perl script, using ESearch and ESummary, to extract
GeneIDs, names and names for a species (i.e. by Taxonomy's id). Usage notes
provided when no arguments are supplied are:
Usage: taxidToGeneNames.pl [option] -t taxonomyId -o xml|tab
Options: -h Display this usage help information
-v Verbose
-o output options
xml - XML
tab - tab-delimited
Output is written to STDOUT.
Sample execution statement:
taxidToGeneNames.pl -t 9615 -o xml > 9615_genes
==========================================================================
ii. gene2xml
---------------------------------------------------------------------------
gene2xml is a standalone program that converts Entrez Gene ASN.1 into XML.
It also interconverts different formats of Entrez Gene ASN.1. It is
available for multiple platforms.
directory path:
ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/cmdline/
gene2xml.linux64.gz
gene2xml.mac.gz
gene2xml.win64.zip
OR
ftp://ftp.ncbi.nlm.nih.gov/asn1-converters/by_program/gene2xml/
linux64.gene2xml.gz
mac.gene2xml.gz
win64.gene2xml.zip
For comprehensive documentation, use either of these sources:
ftp://ftp.ncbi.nlm.nih.gov/asn1-converters/documentation/gene2xml_readme.txt
OR
ftp://ftp.ncbi.nlm.nih.gov/gene/tools/README
===========================================================================
iii. geneDocSum.pl
---------------------------------------------------------------------------
A representative perl script, using ESearch and ESummary, to extract
GeneIDs and other fields from the Document Summary (DocSum). Usage notes
provided when no arguments are supplied are:
Usage: geneDocSum.pl [options] -q query -o xml|tab
Options: -h Display this usage help information
-v Verbose
-q Query to run against Entrez Gene, e.g. "has summary[prop]"
-o Output options
xml - XML
tab - tab-delimited
-t Tag from eutils xml to extract, e.g. "Summary"
- is case sensitive
- may be specified multiple times to extract multiple
tags & values
- used only with "-o tab" option
- to see all available xml tags in the DocSum, run first
with "-o xml" option
Output is written to STDOUT.
Sample execution statement:
geneDocSum.pl -q "has_summary[prop] AND chimpanzee[orgn]" -o tab -t Name -t Summary
===========================================================================
iv. geneGoSummary.pl
---------------------------------------------------------------------------
A representative perl script, using ESearch, to extract a summary of
GeneOntology information. Usage notes provided when no arguments are
supplied are:
Usage: geneGoSummary.pl [options]
Options: -h Display this usage help information
-v Verbose
-i Input file (or - for stdin) with ranges
-g gene2go file
-t tax id
The tax id defaults to 9606 (Homo sapiens).
The gene2go file is specified with the -g argument, and the latest version of
this file must be downloaded and decompressed before running the
geneGoSummary.pl script.
Output is written to STDOUT.
Sample execution statement:
echo chr12:1000000-2000000 | geneGoSummary.pl -g gene2go
==========================================================================
VII. Gene-related files from genome annotation
---------------------------------------------------------------------------
Genome annotation files are available at: ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq