Difference between revisions of "FlyBase:FilesOverview"

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==Introduction==
+
#REDIRECT [[FlyBase:Downloads Overview]]
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The "[http://flybase.org/static_pages/downloads/bulkdata7.html Precomputed data files for the current release]" page (referred to herein as the "Precomputed files" page) lists data files generated from the current release of FlyBase and links to the [ftp://ftp.flybase.net/releases/current/ current FTP repository]. Data from the previous five releases can be found on the "[http://flybase.org/static_pages/downloads/archivedata3.html Archived data files for recent releases]" page (referred to herein as the "Archived data" page), as well as links to servers hosting older releases of FlyBase, and all the release notes and news archives from FB2006_01. If you are looking for old data and cannot find it on the "Archived data" page please follow a link to the [ftp://ftp.flybase.net/releases/ FTP repository].
 
−
 
 
−
===Known Issues===
 
−
 
 
−
Safari does not connect properly to the FlyBase FTP site. You should be able to download individual files using Safari but you will not be able to browse the FTP repository.
 
−
 
 
−
 
 
−
==The FTP archive==
 
−
 
 
−
The "Main Data Set" section of the "[http://flybase.org/static_pages/downloads/bulkdata7.html Precomputed files]" page provides links to FlyBase FTP repository. The "Chado database" link leads to the psql directory of the current FTP repository where you can obtain a dump of the PostgreSQL Chado database. If you have a PostgreSQL client application installed and would like to access the latest FlyBase release without installing the database you can connect to the FlyBase public read only Chado database as:
 
−
 
 
−
$ psql -h flybase.org -U flybase flybase
 
−
 
 
−
The version running on this service is identical to the current web site release.
 
−
 
 
−
The "Drosophila Data" section contains links to other sections of the FTP repository. The data can be accessed either by the version of FlyBase (The "[ftp://ftp.flybase.net/releases/current/ Current FTP repository]") or for sequence data by the annotation release of a particular Drosophila species (see the "[ftp://ftp.flybase.net/genomes/ Genomes FTP archive]")
 
−
 
 
−
==General Information about the Files Available==
 
−
 
 
−
===File Names===
 
−
The first part of a filename always describes the content of the file, for example the file fbgn_annotation_ID_fb_2008_10.tsv.gz maps the primary FlyBase identifiers to the annotation symbols used for genes.
 
−
 
 
−
Many of the precomputed data filenames also contain a release or version number. In the example above "fb_2008_10" denotes version FB2008_10 of FlyBase. Sequence data files, such as dmel-all-CDS-r5.13.fasta.gz, denote the annotation release that the data relates to as '-r5.13'. The 'r5' indicates the data is taken from the release 5 of the sequence assembly and the '13' after the decimal point specifies the annotation release. Please see "[http://flybase.org/static_pages/news/articles/2008_08/flybase_updates.html A more frequent FlyBase update cycle]" for further discussion of the difference between the current release of FlyBase and a genome annotation release.
 
−
 
 
−
The following notation is used for different file formats:
 
−
 
 
−
:'''Tab separated files''' are indicated by the extension ''''.tsv''''
 
−
:'''[http://www.geneontology.org/GO.format.shtml#oboflat OBO format files]''', which are used for the ontologies, are denoted ''''.obo''''
 
−
:'''Plain text''' files are given the extension ''''.txt''''
 
−
:Files containing nucleic acid or polypeptide sequence data in the '''FASTA''' format are listed as ''''.fasta''''
 
−
:'''GFF''' files include the suffix ''''.gff''''
 
−
:'''XML''' data files are denoted ''''.xml''''
 
−
 
 
−
Most of the files listed on the "Precomputed files" page and the "Archived data" page are compressed with the [http://www.gzip.org/ GNU gzip] program. These files end with the suffix '.gz'. The ontology files are compressed in the ZIP file format, as indicated by the suffix '.zip'.
 
−
 
 
−
===Accessing files===
 
−
Files can be downloaded either directly through the web interface, or by using an ftp client such as wget to obtain the file from the FTP repository. Please note that at present Safari fails to connect to the FTP repository correctly, so we recommend that you use another browser if you wish to access the files through the web interface. The ftp client wget accepts wild card patterns which means you can use a query of the following kind to obtain the latest file without having to specify the FlyBase release number:
 
−
 
 
−
$ wget ftp://ftp.flybase.net/releases/current/precomputed_files/genes/fbgn_annotation_ID_*.tsv.gz
 
−
 
 
−
The /releases/current/ path will always point to latest FlyBase release and this directory will have only one copy of the file. Archived copies of the files from previous releases can be obtained by including the FlyBase release in the path /releases/<RELEASE_NUMBER>/. For example to retrieve this file for the FB2008_05 release, type:
 
−
 
 
−
$ wget ftp://ftp.flybase.net/releases/FB2008_05/precomputed_files/genes/fbgn_annotation_ID_*.tsv.gz
 
−
 
 
−
or more specifically:
 
−
 
 
−
$ wget ftp://ftp.flybase.net/releases/FB2008_05/precomputed_files/genes/fbgn_annotation_ID_fb_2008_05.tsv.gz
 
−
 
 
−
===Opening compressed files===
 
−
Microsoft and Apple include built-in ZIP support in later versions of their operating systems. These files can also be opened with the free program [http://www.7-zip.org/ 7-zip].
 
−
 
 
−
On OS X or Unix a GZIP compressed file can be extracted with the gunzip command. On a Windows machine we suggest that you use the program [http://www.7-zip.org/ 7-zip] to open these files, because several people have reported problems using WinZip. You should be able to open and read the resulting file with any text editor.
 
−
 
 
−
 
 
−
==Types of Files Available==
 
−
 
 
−
===XML files===
 
−
 
 
−
These files are generated from the PostgreSQL Chado database for each release of FlyBase. The Chado XML files contain all the information used to generate the report pages and reflect the organization of the data in the database, whereas the Reporting XML files contain a more compact version of the Chado XML. The DTDs for these XML files, listing the structure of the files, are posted in the chado-xml and reporting-xml directories of the FTP repository for each release. For the latest versions of the DTDs please see:
 
−
 
 
−
ftp://ftp.flybase.net/releases/current/chado-xml/
 
−
 
 
−
ftp://ftp.flybase.net/releases/current/reporting-xml/
 
−
 
 
−
The XML files can also be obtained directly from the "Precomputed files" page by clicking on the "download" link under the ChadoXML or Reporting XML headings in the appropriate section. The Chado and Reporting XML files are available for genes, alleles, stocks, transcripts, polypeptides, insertions, transgenic (recombinant) constructs, aberrations, balancers, clones, and references.
 
−
 
 
−
'''Please note:'''
 
−
 
 
−
The chado_genes.xml.gz file is used to generate the FlyBase gene report pages. Data for the [http://gmod.org/wiki/Common_Gene_Page GMOD Common Gene Page] project is provided in the chado_common_gene_page.xml.gz file, which is only available as [ftp://ftp.flybase.net/releases/current/chado-xml/ Chado XML from the FTP repository].
 
−
 
 
−
 
 
−
===Ontology Files===
 
−
 
 
−
The [http://flybase.org/static_pages/docs/refman/refman-G.html#G.2. controlled vocabularies] (aka ontologies) used by FlyBase are available under the Ontology Terms section of the "[http://flybase.org/static_pages/downloads/bulkdata7.html Precomputed files]" page. Each controlled vocabulary is described in detail in [http://flybase.org/static_pages/docs/refman/refman-G.html#G.2. section G.2]. of the Reference Manual. The files are in the [http://www.geneontology.org/GO.format.shtml#oboflat OBO format] used by the [http://www.obofoundry.org/ Open Biomedical Ontology] group, and are designed to be used with the free [http://www.oboedit.org/ OBO-Edit] tool.
 
−
 
 
−
Controlled vocabularies undergo continual development; terms and definitions are refined, added, merged, split and obsoleted in an effort to improve the way they represent their various subjects. On the "[http://flybase.org/static_pages/downloads/bulkdata7.html Precomputed files]" page the frozen versions of the controlled vocabularies used for the current release of FlyBase are available, and there are also links to the current 'live' versions maintained by the [http://www.obofoundry.org/ Open Biomedical Ontology] group.
 
−
 
 
−
Frozen versions of the controlled vocabularies used for previous releases of FlyBase are available on the "[http://flybase.org/static_pages/downloads/archivedata3.html Archived data]" page, and in the following directories of the FTP repository:
 
−
 
 
−
ftp://ftp.flybase.net/releases/<RELEASE_NUMBER>/precomputed_files/ontologies/
 
−
 
 
−
For example see:
 
−
 
 
−
ftp://ftp.flybase.net/releases/FB2008_03/precomputed_files/ontologies/
 
−
 
 
−
===FASTA Files===
 
−
 
 
−
The FlyBase FASTA files generally follow the [http://en.wikipedia.org/wiki/Fasta_format FASTA format] guidelines with one exception being that our header lines sometime exceed the 80 character limit. The FASTA filenames follow these formats:
 
−
 
 
−
'''dmel-all-<data type>-r<release-number>.fasta.gz'''
 
−
 
 
−
or
 
−
 
 
−
'''dmel-<chromosome_arm>-<data_type>-r<release-number>.fasta.gz'''
 
−
 
 
−
Where '''data_type''' is one of the following entries in the table below. The '''all''' files contain sequences for those data types on all chromosome arms whereas the specific chromosome arm have only those features for that particular chromosome.
 
−
 
 
−
{| class= "wikitable"
 
−
!Data Type
 
−
!Content Description
 
−
|-
 
−
|'''aligned '''
 
−
|The region of genomic sequence that analysis features align to.
 
−
|-
 
−
|'''CDS'''
 
−
|The contiguous protein coding sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.
 
−
|-
 
−
|'''chromosome'''
 
−
|The sequence of each chromosome arm.
 
−
|-
 
−
|'''clones'''
 
−
|The sequence of full length cDNA, 3' and 5' ESTs, and partial length clones.
 
−
|-
 
−
|'''exon '''
 
−
|The sequence of each exon split up into individual FASTA records.
 
−
|-
 
−
|'''five_prime_UTR'''
 
−
|The sequence of 5' untranslated regions.
 
−
|-
 
−
|'''gene'''
 
−
|The sequence of the gene span.
 
−
|-
 
−
|'''gene_extended2000'''
 
−
|The sequence of the gene span with 2000 base pairs added upstream and downstream.
 
−
|-
 
−
|'''intergenic'''
 
−
|The sequence of chromosomal regions between genes that do not contain known gene models.
 
−
|-
 
−
|'''intron'''
 
−
|The sequence of each intron split up into individual FASTA records.
 
−
|-
 
−
|'''miRNA'''
 
−
|The sequence of transcripts that are typed as micro RNAs.
 
−
|-
 
−
|'''miscRNA'''
 
−
|The sequence of transcripts that are typed as small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), or ribosomal RNA (rRNA). May also contain other transcript types that do not exist in their own individual files.
 
−
|-
 
−
|'''ncRNA'''
 
−
|The sequence of transcripts that are typed as non coding RNAs (ncRNA).
 
−
|-
 
−
|'''predicted'''
 
−
|The sequence of various features that are derived from a variety of prediction algorithms. These can encompass analyses conducted by FlyBase or by 3rd party groups.
 
−
|-
 
−
|'''pseudogene'''
 
−
|The sequence of transcripts that are typed as pseudogenes.
 
−
|-
 
−
|'''sequence_features'''
 
−
|The sequence of sequence features, which currently describe data about RNAi reagents. In the future, it will also contain natural genomic features (aside from transcribed regions), such as replication origins, transcription factor binding sites and boundary elements, and other experimental reagents that map to the genome, such as microarray oligonucleotides and rescue fragments.
 
−
|-
 
−
|'''synteny'''
 
−
|The sequence of syntenic regions between two species.
 
−
|-
 
−
|'''three_prime_UTR'''
 
−
|The sequence of 3' untranslated regions.
 
−
|-
 
−
|'''transcript'''
 
−
|The sequence of transcripts that are typed as messenger RNAs (mRNA).
 
−
|-
 
−
|'''translation'''
 
−
|The resulting protein sequence from protein coding transcripts.
 
−
|-
 
−
|'''transposon'''
 
−
|The sequence of transposable elements.
 
−
|-
 
−
|'''tRNA'''
 
−
|The sequence of transcripts that are typed as transfer RNAs (tRNA).
 
−
|}
 
−
 
 
−
 
 
−
'''FASTA header format'''
 
−
 
 
−
The typical format of our FASTA header begins with an ID followed by any number of fields that follow this format
 
−
 
 
−
'''field_name=value;'''
 
−
 
 
−
Multiple field values are separated by commas
 
−
 
 
−
'''field_name=value1,value2;'''
 
−
 
 
−
This table describes some of the field names found in our FASTA headers
 
−
 
 
−
{|class = "wikitable"
 
−
 
 
−
!Field Name
 
−
!Description
 
−
|-
 
−
|'''type'''
 
−
|The feature type of the FASTA sequence record.
 
−
|-
 
−
|'''loc'''
 
−
|The genomic location given in the NCBI's feature location format. Please see the [ftp://ftp.ncbi.nih.gov/genbank/docs/ NCBI's] site for more information.
 
−
|-
 
−
|'''ID'''
 
−
|A unique ID. IDs in the form of FBxx[0-9]+ are a unique FlyBase object identifier.
 
−
|-
 
−
|'''name'''
 
−
|The name or symbol of the feature.
 
−
|-
 
−
|'''dbxref'''
 
−
|Database cross references relating to the FASTA record. The dbxref values use a 'dbname:dbid' format.
 
−
|-
 
−
|'''MD5'''
 
−
|An [http://en.wikipedia.org/wiki/MD5 MD5] checksum calculated from the sequence that can be used to identify identical sequences.
 
−
|-
 
−
|'''length'''
 
−
|The length of the sequence found in the FASTA record.
 
−
|-
 
−
|'''release'''
 
−
|The release number denotes the annotation release which this FASTA record corresponds to.
 
−
|-
 
−
|'''species'''
 
−
|The species abbreviation that this FASTA record corresponds to.
 
−
|}
 
−
 
 
−
 
 
−
===GFF Files===
 
−
 
 
−
The FlyBase GFF files follow the [http://www.sequenceontology.org/gff3.shtml GFF v3] specification. The GFF files contain feature line definitions for gene models, predicted features, alignments, and many other features. The GFF files are produced for each species and can be downloaded from our FTP site using this URL form:
 
−
 
 
−
ftp://ftp.flybase.net/genomes/<species abbreviation>/current/gff/
 
−
 
 
−
e.g. ftp://ftp.flybase.net/genomes/dmel/current/gff/
 
−
 
 
−
For melanogaster, there are 3 GFF files distributed, they include:
 
−
 
 
−
:'''dmel-all-r<release-number>.gff.gz'''
 
−
::Contains all chromosome arms
 
−
:'''dmel-all-no-analysis-r<release-number>.gff.gz'''
 
−
::Same as above except all match and match_part features have been removed
 
−
:'''dmel-<chromosome_arm>-r<release-number>.gff.gz'''
 
−
::Contains only a single chromosome arm as identifed by the filename
 
−
 
 
−
The other species have the all chromosome arm file and also a tar and gzipped file containing the individual scaffolds. Please note that the tarball contains thousands of files in a single directory level so extracting them may result in filesystem performance issues.
 
−
 
 
−
===Precomputed Data Text Files===
 
−
 
 
−
Precomputed data files that contain useful sets of data are generated for every release of FlyBase. For example, the file fbgn_NAseq_Uniprot_fb_2008_10.tsv.gz contains the mapping between valid FlyBase Identifiers and the corresponding nucleic acid and protein accession numbers used by DDBJ/EMBL/GenBank and UniprotKB/Swiss-Prot/TrEMBL. These files can be found under the "Other" heading of each section of the "[http://flybase.org/static_pages/downloads/bulkdata7.html Precomputed files]" and "[http://flybase.org/static_pages/downloads/archivedata3.html Archived data]" pages, and are also available under the precomputed_files directory of each FlyBase release in the [ftp://ftp.flybase.net/releases/ FTP repository].
 
−
 
 
−
Superscripts and subscripts are represented in the precomputed data files in the ASCII text format used by FlyBase, which is described in [[FlyBase:Nomenclature#10.3|section 10.3]] of the Nomenclature document.
 
−
 
 
−
At the top and bottom of each tab separated text file there are a few lines that describe the file. These lines start with a '#' symbol. The line immediately before the start of the data contains headings for each of the tab separated columns in the file. The file can also include some blank lines to separate information about the version of the file from the description of data in the file.
 
−
 
 
−
Each precomputed data file available for download on the "[http://flybase.org/static_pages/downloads/bulkdata7.html Precomputed files]" page contains the complete data set for the FlyBase release. Please note, if you are only looking for information on a defined subset of genes, or other FlyBase data type, you can query the current set of precomputed data files through the [http://flybase.org/static_pages/downloads/ID.html Batch Download] tool to obtain the data you require. This approach is described in more detail in the "How to Download Field Data" section of the help document at the bottom of the [http://flybase.org/static_pages/downloads/ID.html Batch Download] page.
 
−
 
 
−
==Contents of the Precomputed Data Text Files listed by Section==
 
−
 
 
−
===Synonyms===
 
−
====FlyBase Synonyms (fb_synonym_*.tsv)====
 
−
The file reports current symbols and synonyms for the following objects in FlyBase: genes, alleles, balancers, aberrations, insertions, recombinant constructs, transcripts, and proteins.
 
−
 
 
−
The file includes:
 
−
 
 
−
:nuclear genes located to the sequence
 
−
:mitochondrial genes
 
−
:genes not located to the sequence
 
−
 
 
−
Columns are:
 
−
 
 
−
#Primary FlyBase identifier for the object
 
−
#Current symbol used in FlyBase for the object
 
−
#Current full name used in FlyBase for the object
 
−
#Non-current full name(s) associated with the object
 
−
#Non-current symbol(s) associated with the object
 
−
 
 
−
===Genes===
 
−
====Genetic Interaction table (gene_genetic_interactions_*.tsv)====
 
−
The file reports the summary of gene-level genetic interactions curated in FlyBase. This is the data reported in the "Summary of Genetic Interactions" section of the gene report pages.
 
−
 
 
−
The file includes the following Dmel genes:
 
−
 
 
−
:nuclear genes located to the sequence
 
−
:genes not located to the sequence
 
−
 
 
−
it excludes:
 
−
 
 
−
:mitochondrial genes
 
−
 
 
−
Columns are:
 
−
 
 
−
#Current FlyBase gene symbol
 
−
#Current FlyBase identifier (FBgn#) of gene
 
−
#Current symbol of interacting gene
 
−
#Current FlyBase identifier (FBgn#) of interacting gene
 
−
#Allele(s) of gene in column 1 that have been shown to interact with gene in column 3.
 
−
#Current FlyBase identifer (FBrf#) of publication from which data came
 
−
 
 
−
====FBgn <=> DB Accession IDs (fbgn_NAseq_Uniprot_*.tsv)====
 
−
The file reports EMBL/GenBank/DDBJ nucleotide and protein accessions, and UniProtKB/SwissProt/TrEMBL protein accessions associated with FlyBase genes.
 
−
 
 
−
The file includes:
 
−
 
 
−
:nuclear genes with sequence accession numbers
 
−
:mitochondrial genes
 
−
 
 
−
it excludes:
 
−
 
 
−
:genes without sequence accession numbers
 
−
 
 
−
Columns are:
 
−
 
 
−
#Current symbol of gene
 
−
#Current FlyBase identifier (FBgn#) of gene
 
−
#EMBL/GenBank/DDBJ nucleotide accession associated with the gene
 
−
#EMBL/GenBank/DDBJ protein accession(s) associated with the gene and nucleotide accession in column 3.
 
−
#UniProtKB/SwissProt/TrEMBL protein accession associated with the gene
 
−
 
 
−
Each row contains information about a single accession associated with a gene, thus if a gene has multiple accessions associated with it, multiple rows will exist for that gene in the file.
 
−
 
 
−
A single row contains '''either''' information about a EMBL/GenBank/DDBJ accession '''or''' information about a UniProtKB/SwissProt/TrEMBL accession, not both.
 
−
 
 
−
For rows containing information about a EMBL/GenBank/DDBJ accession, a nucleotide accession associated with the gene is listed in column 3. If there is also a EMBL/GenBank/DDBJ protein accession associated with that gene '''and''' with the nucleotide accession in column 3., this protein accession is listed in column 4. In this case, column 5. is always empty.
 
−
 
 
−
For rows containing information about a UniProtKB/SwissProt/TrEMBL protein accession, a protein accession associated with the gene is listed in column 5. In this case, columns 3. and 4. are always empty.
 
−
 
 
−
====FBgn <=> Annotation ID (fbgn_annotation_ID_*.tsv)====
 
−
 
 
−
The file reports current and secondary FlyBase identifiers associated with FlyBase genes, including current and secondary gene identifiers (FBgn#), and current and secondary annotation identifiers (CG#).
 
−
 
 
−
The file includes:
 
−
 
 
−
:nuclear genes located to the sequence
 
−
:mitochondrial genes
 
−
 
 
−
it excludes:
 
−
 
 
−
:genes not located to the sequence
 
−
 
 
−
Columns are:
 
−
 
 
−
#Current symbol of gene
 
−
#Current FlyBase identifier (FBgn#) of gene
 
−
#Secondary FlyBase identifier(s) (FBgn#) associated with the gene
 
−
#Current annotation identifier associated with the gene
 
−
#Secondary annotation identifier(s) associated with the gene
 
−
 
 
−
'''Please Note:''' If a gene has multiple secondary identifiers, all the values are stored within one tab separated column and are separated by commas (for example as: FBgn0034701,FBgn0034702).
 
−
 
 
−
====FBgn <=> GLEANR IDs (fbgn_gleanr_*.tsv)====
 
−
 
 
−
This file reports the relationship between the symbols and gene identifiers used by FlyBase for non-melanogaster genes identified by the AAA consortium, and the GLEANR identifier assigned to the gene during the initial annotation of the genome sequence.
 
−
 
 
−
The file includes:
 
−
 
 
−
:non-melanogaster genes located to the sequence
 
−
 
 
−
it excludes:
 
−
 
 
−
:''D. melanogaster'' genes
 
−
:non-melanogaster genes not located to the sequence
 
−
 
 
−
Columns are:
 
−
 
 
−
#Current FlyBase gene symbol
 
−
#Current FlyBase identifier (FBgn#) of the gene
 
−
#GLEANR identifier assigned by the AAA Consortium.
 
−
 
 
−
====FBgn <=> FBtr <=> FBpp IDs (fbgn_fbtr_fbpp_*.tsv)====
 
−
 
 
−
This file reports the relationship of gene identifiers used by FlyBase for sequence localized genes, and the identifiers used for the transcript and polypeptide products of these genes.
 
−
 
 
−
The file includes:
 
−
 
 
−
:genes located to the sequence
 
−
 
 
−
it excludes:
 
−
 
 
−
:genes not located to the sequence
 
−
 
 
−
Columns are:
 
−
 
 
−
#Current FlyBase identifier (FBgn#) of the gene
 
−
#Current FlyBase identifier (FBtr#) of a transcript encoded by the gene listed in column 1.
 
−
#Current FlyBase identifier (FBpp#) of a polypeptide encoded by the transcript listed in column 2, where this is relevant.
 
−
 
 
−
====FBgn Exons <=> Affy1 (fbgn_exons2affy1_overlaps.tsv)====
 
−
 
 
−
The file is generated by testing for overlaps, no matter how small, of the locations of Affy1 oligos in the genome with the locations of gene exons, as defined by the '''Dmel''' gene models for the current release of FlyBase. If the location of an Affy1 oligo shows any kind of overlap with an exon of a gene, a Gene=>Affy reference is recorded in this file.
 
−
 
 
−
The extent of the overlap has no influence on the inclusion of a crossreference in this file. The overlap might be just one nucleotide, or it could be an exact match to the exon. For interpretation of the significance of a partial overlap please contact Affymetrix.
 
−
 
 
−
The file includes the following '''Dmel''' genes:
 
−
 
 
−
:nuclear genes located to the sequence
 
−
 
 
−
it excludes:
 
−
 
 
−
:genes not located to the sequence
 
−
:mitochondrial genes
 
−
 
 
−
Each line of the file '''can contain many''' tab separated columns:
 
−
 
 
−
'''The first column of a line''' contains the valid [http://flybase.org/static_pages/docs/refman/refman-F.html#F.1. FlyBase identifier] of a gene.
 
−
'''Subsequent columns:''' Each '''Affy1 ID''' that overlaps with an exon of the gene, as described above, is listed in an additional tab separated column. Thus, this file does not contain a predefined number of columns.
 
−
 
 
−
====FBgn Exons <=> Affy2 (fbgn_exons2affy2_overlaps.tsv)====
 
−
 
 
−
The file is generated from the location of Affy2 oligos exactly as described for Affy1 oligos above.
 
−
Genes GO data (gene_association.fb)
 
−
 
 
−
The file contains the Gene Ontology (GO) controlled vocabulary (CV) terms assigned to FlyBase genes.
 
−
 
 
−
The file includes the following Dmel genes:
 
−
 
 
−
:nuclear genes located to the sequence
 
−
:mitochondrial genes
 
−
:genes not located to the sequence
 
−
 
 
−
The columns of the file are described in section G.3.1. of the Reference manual.
 
−
Genes map table (gene_map_table_*.tsv)
 
−
 
 
−
The file reports available localization information for FlyBase genes.
 
−
 
 
−
It includes:
 
−
 
 
−
:nuclear genes located to the sequence
 
−
:mitochondrial genes
 
−
:genes not located to the sequence
 
−
 
 
−
Columns are:
 
−
 
 
−
#Current FlyBase gene symbol
 
−
#Current FlyBase identifier (FBgn#) of gene
 
−
#recombination map location
 
−
#cytogenetic location
 
−
#genomic location
 
−
 
 
−
====Gene summaries (gene_summaries.tsv)====
 
−
 
 
−
The file contains the summaries found on gene report pages and the pop-ups in GBrowse and Interactions Browser in plain text.
 
−
 
 
−
It includes:
 
−
 
 
−
:nuclear genes located to the sequence
 
−
:mitochondrial genes
 
−
:genes not located to the sequence
 
−
 
 
−
The tab delimited file contains two columns:
 
−
 
 
−
#FlyBase ID. The Valid FlyBase identifier number for the gene.
 
−
#The gene summary as a string of plain text.
 
−
 
 
−
====Orthologs (gene_orthologs_fb_*.tsv.gz)====
 
−
 
 
−
The file reports D. melanogaster genes and their orthologs in other sequenced strains.
 
−
 
 
−
The file includes:
 
−
 
 
−
:nuclear genes located to the sequence
 
−
 
 
−
it excludes:
 
−
 
 
−
:genes not located to the sequence
 
−
:mitochondrial genes
 
−
 
 
−
Columns are:
 
−
 
 
−
#Current FlyBase identifier (FBgn#) of ''D. melanogaster'' gene
 
−
#Current FlyBase gene symbol ''D. melanogaster'' gene
 
−
#Arm upon which ''D. melanogaster'' gene is localized
 
−
#Location of ''D. melanogaster'' gene on the arm
 
−
#Strand of ''D. melanogaster'' gene
 
−
#Current FlyBase identifier (FBgn#) of non-melanogaster orthologous gene
 
−
#Current FlyBase gene symbol of non-melanogaster orthologous gene
 
−
#Arm upon which non-melanogaster orthologous gene is localized
 
−
#Location of non-melanogaster orthologous gene on the arm
 
−
#Strand of non-melanogaster orthologous gene
 
−
 
 
−
====Unique Protein Isoforms (dmel_unique_protein_isoforms_fb_*.tsv.gz)====
 
−
 
 
−
The file reports ''D. melanogaster'' genes and their unique protein isoforms.
 
−
 
 
−
The file includes:
 
−
 
 
−
:melanogaster genes located to the sequence
 
−
 
 
−
it excludes:
 
−
 
 
−
:melanogaster genes not located to the sequence
 
−
:non-melanogaster genes
 
−
 
 
−
Columns are:
 
−
 
 
−
:Current FlyBase identifier (FBgn#) of the D. melanogaster gene
 
−
:Current FlyBase gene symbol of the D. melanogaster gene
 
−
:Current FlyBase protein symbol of the representative protein isoform.
 
−
:Current FlyBase protein symbol(s) of identical protein isoforms.
 
−
 
 
−
===Alleles and Stocks===
 
−
====Stock data (eg. stocks_FB2008_10.tsv)====
 
−
 
 
−
This file reports genetic components and related information about Stocks in FlyBase. The following provides a brief description of the columns in the file:
 
−
#FBst. The unique identifier assigned to this stock by FlyBase. Example: FBst0025115
 
−
#collection_short_name. A short name for the stock collection that holds the stock. Example: Szeged
 
−
#stock_type_cv. The controlled vocabulary term and unique identifier that describe the state of the stock. Example: living_stock ; FBcv:0010000
 
−
#species. The FlyBase four-letter [http://flybase.org/static_pages/docs/abbreviations.html abbreviation] for the species of the stock. Example: Dmel
 
−
#FB_genotype. Genetic components of the stock corresponding to alleles, aberrations, balancers, or insertions in FlyBase. May be empty. Example: P{EP}wun2[EP2217]
 
−
#description. Genetic components of the stock as provided to FlyBase by the collection that holds the stock. Example: EP(2)2217
 
−
#stock_number. The stock identifier provided to FlyBase by the collection that holds the stock. May be empty. Example: 0000-1006.01
 
−
 
 
−
====Genetic Interactions (allele_genetic_interactions_*.tsv)====
 
−
 
 
−
The file reports controlled vocabulary (i.e. not free text) genetic interaction data associated with alleles. This is the data reported in the "Phenotypic Class" and "Phenotype Manifest in" subsections of the "Interactions" section of each Allele Report.
 
−
 
 
−
Columns are:
 
−
 
 
−
#Current FlyBase allele symbol
 
−
#Current FlyBase identifier (FBal#) of allele
 
−
#Interaction information associated with allele
 
−
#Current FlyBase identifer (FBrf#) of publication from which data came
 
−
 
 
−
====Phenotypic data (allele_phenotypic_data_*.tsv)====
 
−
 
 
−
The file reports controlled vocabulary (i.e. not free text) phenotypic data associated with alleles. This is the data reported in the "Phenotypic Class" and "Phenotype Manifest in" subsections of the "Phenotypic Data" section of each Allele Report.
 
−
 
 
−
Columns are:
 
−
 
 
−
#Current FlyBase allele symbol
 
−
#Current FlyBase identifier (FBal#) of allele
 
−
#Phenotypic data associated with allele
 
−
#Current FlyBase identifer (FBrf#) of publication from which data came
 
−
 
 
−
===Nomenclature===
 
−
====Species abbreviation list (species-abbreviations.txt)====
 
−
 
 
−
The species-abbreviations.txt file lists all the species for which FlyBase has some information. FlyBase includes gene reports for genes derived from species within the family Drosophilidae, as well as gene reports for non-drosophilid genes ("foreign genes") that have been introduced into Drosophila via transgenic constructs and for engineered objects such as a fusion gene between two ''D.melanogaster'' genes. In addition, information about non-Drosophilid species is also displayed in GBrowse, for example in the "Similarity: Proteins" evidence tier. Thus, the file contains information for both Drosophilid and non-Drosophilid species.
 
−
 
 
−
There are 8 columns of data in the file, each separated by " | ".
 
−
 
 
−
#Internal_id. The Primary [http://flybase.org/static_pages/docs/refman/refman-F.html#F.1. FlyBase identifier number] of the organism.
 
−
#Taxgroup. A grouping term, currently one of "drosophilid", "non-drosophilid eukaryote", "prokaryote", "transposable element" or "virus".
 
−
#Abbreviation. The standard FlyBase prefix for the species. This abbreviation is used in FlyBase as the first part of the symbol (before the '\') of any object, e.g. a gene or allele, that originates from this species. This column may be blank, if data from a species is displayed in an evidence tier on [http://flybase.org/cgi-bin/gbrowse/dmel/ GBrowse] but no individual report page exists for that species in FlyBase.
 
−
#Genus. The genus name of the organism.
 
−
#Species name. The species name of the organism.
 
−
#Common name. The common name of the organism. This column may be blank.
 
−
#Comment. A free text field for additional comments. This column may be blank.
 
−
#Ncbi-taxon-id. The [http://www.ncbi.nlm.nih.gov/taxonomy NCBI Taxonomy Database] Taxon ID for the organism. This column may be blank.
 
−
 
 
−
An html version of this file is also available - see the [http://flybase.org/static_pages/docs/abbreviations.html Species Abbreviations] page.
 
−
===Transposons, Transgenic Constructs, and Insertions===
 
−
====Transgenic construct maps (construct_maps.zip)====
 
−
 
 
−
The construct_maps.zip file unpacks as a directory containing maps of recombinant constructs and transgenic transposons generated by FlyBase, that are based on the compiled sequence data curated by FlyBase. The name of each PNG image in the directory corresponds to the [http://flybase.org/static_pages/docs/refman/refman-F.html#F.1. FlyBase identifier] of the respective recombinant construct or transgenic transposon.
 
−
 
 
−
'''Please note:''' For transgenic transposons, the image may be a map of the corresponding plasmid form.
 
−
Map data for insertions (insertion_mapping_*.tsv)
 
−
 
 
−
The insertion mapping table reports available localization information for '''Dmel''' insertions.
 
−
 
 
−
Columns are:
 
−
 
 
−
#Current symbol of insertion
 
−
#Current FlyBase identifier (FBti#) of insertion
 
−
#Genomic location of insertion
 
−
#Range (t/f) indicates whether genomic location is range or single base
 
−
#Orientation (1/0) indicates orientation of insertion on chromosome
 
−
#Estimated cytogenetic location based on correlation of genomic location and estimated genomic location of cytological bands
 
−
#Observed cytogenetic location reported in the literature
 
−
 
 
−
====Transposable elements (canonical set) (transposon_sequence_set.embl.txt)====
 
−
 
 
−
This is a file of 'canonical' sequences of the transposable elements from Drosophila maintained by M. Ashburner.
 
−
 
 
−
The first section of the file outlines the history and revisions to the file and also lists the current set of elements, their size and whether the subsequent sequence data is complete.
 
−
 
 
−
The second section of the file, which is separated from the first by a line of "_" characters contains the sequence data of all the elements in [ftp://ftp.ebi.ac.uk/pub/databases/embl/doc/FT_current.html EMBL format]. The record for each element starts with a line prefixed by "ID" and ends with a line containing "//".
 
−
 
 
−
===Clones===
 
−
====cDNAs: FBcl <=> acc. ID (cDNA_clone_data_*.tsv)====
 
−
 
 
−
The file reports basic cDNA clone data in FlyBase.
 
−
 
 
−
Columns are:
 
−
 
 
−
#Current FlyBase identifier (FBcl#) of cDNA clone
 
−
#Clone name
 
−
#Name of library associated with clone
 
−
#EMBL/GenBank/DDBJ cDNA accession number
 
−
#EMBL/GenBank/DDBJ EST accession number
 
−
 
 
−
Each row contains information about a single cDNA or EST associated with a gene, thus if a gene has multiple cDNAs or ESTs associated with it, multiple rows will exist for that gene in the file.
 
−
 
 
−
A single row contains '''either''' information about a cDNA associated with the gene in column 1 '''or''' information about an EST associated with the gene in column 1, not both.
 
−
 
 
−
====Genomic: FBcl <=> acc. ID (genomic_clone_data_*.tsv)====
 
−
 
 
−
The file reports basic genomic clone data in FlyBase.
 
−
 
 
−
Columns are:
 
−
 
 
−
#Current FlyBase identifier (FBcl#) of genomic clone
 
−
#Clone name
 
−
#EMBL/GenBank/DDBJ accession number
 
−
 
 
−
===Map Conversion Tables===
 
−
====Cytological <=> Sequence (genome-cyto-seq.txt)====
 
−
 
 
−
This is a tab delimited file that FlyBase uses to relate sequence coordinates from release 5 of the ''Drosophila melanogaster'' sequence assembly to published cytogenetic map positions. A description of how this is calculated is provided in [http://flybase.org/static_pages/docs/refman/refman-G.html#G51 section G.5.1.] of the Reference manual.
 
−
 
 
−
The data for each chromosome arm is separated by a line starting with a '#' that lists the name of the chromosome arm and corresponding sequence scaffold.
 
−
 
 
−
The columns in the file are:
 
−
 
 
−
#Cytogenetic map position as described by Bridges.
 
−
#First sequence coordinate for this map position in the sequence scaffold corresponding this chromosome arm.
 
−
#Last sequence coordinate for this map position in the sequence scaffold corresponding this chromosome arm.
 
−
 
 
−
====Cytological <=> Genetic (cytotable.txt)====
 
−
 
 
−
This is the table that FlyBase uses to infer a genetic map position from a published cytogenetic map position for Drosophila melanogaster.
 
−
 
 
−
The first six lines of the file describe the contents of the file or are blank. The data in the file is organized with the cytological position in first four characters of a line followed by a run of spaces and then the genetic map position.
 
−
Cyto <=> Genetic <=> Seq (cyto-genetic-seq.tsv)
 
−
 
 
−
This is a tab separated file generated from the cytotable.txt and genome-cyto-seq.txt files that infers the relationship between published cytogenetic map positions, genetic map positions and release 5 sequence assembly coordinates for ''Drosophila melanogaster''. Please note that band numbers are not given in this file because they are absent in cytotable.txt.
 
−
 
 
−
#Cytogenetic map position
 
−
#Genetic map position
 
−
#Sequence coordinates (release 5) for the interval
 
−
 
 
−
An html version of this file is also available - see the [http://flybase.org/static_pages/docs/cytotable3.html Map Conversion Table] page.
 
−
Genes map table (gene_map_table_fb_*.tsv)
 
−
 
 
−
This is identical to the file listed under the genes section above.
 

Latest revision as of 15:45, 14 September 2015

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