flybasedownloads 2.0.0

Wrapped to download Flybase data with Python, easily and quickly.

FlyBaseDownloads

Python package to facilitate the data download from FlyBase. Most of the available data from their official wiki can be downloaded. One of the purposes of this library is to organize the data as closely as possible to the source, FlyBase. Despite not being the official package, it is organized by data class/type and provides direct downloads of the current bulk data files from the FTP site. For more information, visit the official FlyBase wiki.

• Usage and Installation
• Synonyms
• Genes
  • Genetic interaction table
  • RNA-Seq RPKM values
  • RNA-Seq RPKM values matrix
  • Single Cell RNA-Seq Gene Expression
  • Physical interaction MITAB file
  • Functional complementation table
  • FBgn to DB Accession IDs
  • FBgn to Annotation ID
  • FBgn to GLEANR IDs
  • FBgn to FBtr to FBpp IDs
  • FBgn to FBtr to FBpp IDs (expanded)
  • FBgn exons to Affy1
  • FBgn exons to Affy2
  • Genes Sequence Ontology (SO) data
  • Genes map table
  • Best gene summaries
  • Automated gene summaries
  • Gene Snapshots
  • Unique protein isoforms
  • Non-coding RNAs
  • Enzyme
• Gene Ontology annotation files GO
  • Gene Association File - GAF
• Gene Groups
  • Gene group data
  • Gene groups with HGNC IDs
  • Pathway group
• Alleles and Stocks
  • Stock
  • Genetic interactions
  • Phenotypic
  • Alleles to Genes
• Homologs
  • Drosophila Paralogs
  • Human Orthologs
• Human disease
  • Human disease model
  • Human Orthologs
• Organisms
  • Species list
• Ontology Terms
  • Fly Anatomy
  • Fly Development
  • Flybase Controlled Vocabulary
  • Fly Stock Ontology
  • Gene Ontology
  • Image Ontology
  • Human Disease Ontology
• Insertions
  • Map data for insertions
  • Frequently-used GAL4 drivers table
• Clones
  • cDNAs: FBcl to acc. ID
  • Genomic: FBcl to acc. ID
• References
  • FlyBase FBrf to PubMed ID to PMCID to DOI

Usage and Installation

In order to simplify the download of FlyBase files, the names have been kept as close as possible. To access the data, follow these steps:

1. Install the library using the pip command.

   pip install FlyBaseDownloads

2. Import the library into your file.

   import FlyBaseDownloads as FBD

3. Access the different classes of the library described below.

Synonyms

To download the file, execute the following command.

Synonyms = FBD.Synonyms.get()

The file reports current symbols and synonyms for the following objects in FlyBase: genes (FBgn), alleles (FBal), balancers (FBba), aberrations (FBab), transgenic constructs (FBtp), insertions (FBti), transcripts (FBtr), and proteins (FBpp).

Columns Description

Column heading	Content Description
primary_FBid	Primary FlyBase identifier for the object
organism_abbreviation	Abbreviation (from the Species Abbreviations list) indicating the species of origin
current_symbol	Current symbol used in FlyBase for the object
current_fullname	Current full name used in FlyBase for the object
fullname_synonym(s)	Non-current full name(s) associated with the object (pipe separated values)
symbol_synonym(s)	Non-current symbol(s) associated with the object (pipe separated values)

Genes

To facilitate its usage, it is suggested to access the data using the following command.

Genes = FBD.Genes

Then, enter the specific method according to the desired data

Genetic interaction table

To download the file, execute the following command.

Genetic_interaction_table = Genes.Genetic_interaction_table()

Columns Description

Column heading	Content Description
Starting_gene(s)_symbol	Current FlyBase symbol of gene(s) involved in the starting genotype
Starting_gene(s)_FBgn	Current FlyBase identifier (FBgn#) of gene(s) involved in the starting genotype
Interacting_gene(s)_symbol	Current FlyBase symbol of gene(s) involved in the interacting genotype
Interacting_gene(s)_FBgn	Current FlyBase identifier (FBgn#) of gene(s) involved in the interacting genotype
Interaction_type	Type of interaction observed, either 'suppressible' or 'enhanceable'
Publication_FBrf	Current FlyBase identifier (FBrf#) of publication from which the data came

RNA-Seq RPKM values

To download the file, execute the following command.

RNASeq_values = Genes.RNASeq_values()

Columns Description

Column heading	Content Description
Release_ID	The D. melanogaster annotation set version from which the gene model used in the analysis derives
FBgn#	The unique FlyBase gene ID for this gene
GeneSymbol	The official FlyBase symbol for this gene
Parent_library_FBlc#	The unique FlyBase ID for the dataset project to which the RNA-Seq experiment belongs
Parent_library_name	The official FlyBase symbol for the dataset project to which the RNA-Seq experiment belongs
RNASource_FBlc#	The unique FlyBase ID for the RNA-Seq experiment used for RPKM expression calculation
RNASource_name	The official FlyBase symbol for the RNA-Seq experiment used for RPKM expression calculation
RPKM_value	The RPKM expression value for the gene in the specified RNA-Seq experiment
Bin_value	The expression bin classification of this gene in this RNA-Seq experiment, based on RPKM value. Bins range from 1 (no/extremely low expression) to 8 (extremely high expression)
Unique_exon_base_count T	he number of exonic bases unique to the gene (not overlapping exons of other genes). Field will be blank for genes derived from dicistronic/polycistronic transcripts
Total_exon_base_count	The number of bases in all exons of this gene
Count_used	Indicates if the RPKM expression value was calculated using only the exonic regions unique to the gene and not overlapping exons of other genes (Unique), or, if the RPKM expression value was calculated based on all exons of the gene regardless of overlap with other genes (Total). RPKM expression values are typically reported for the "Unique" count, except for genes on dicistronic/polycistronic transcripts, in which case the "Total" count is reported

RNA-Seq RPKM values matrix

To download the file, execute the following command.

RNASeq_values_matrix = Genes.RNASeq_values_matrix()

Columns Description

Column heading	Content Description
gene_primary_id	The unique FlyBase gene ID for this gene.
gene_symbol	The official FlyBase symbol for this gene.
gene_fullname	The official full name for this gene.
gene_type	The type of gene: e.g., protein_coding_gene, non_protein_coding_gene.
DATASAMPLE_NAME_(DATASET_ID)	Each subsequent column reports the gene RPKM values for the sample listed in the header. The dataset "FBlc" ID is listed in parentheses, and can be pasted into FlyBase search to access more information on the sample from the "dataset" report.

Single Cell RNA-Seq Gene Expression

To download the file, execute the following command.

SingleCellRNASeq_Gene_Expression = Genes.Single_Cell_RNA_Gene_Expression()

Columns Description

Column heading	Content Description
Pub_ID	The FlyBase FBrf ID for the reference in which the expression was reported.
Pub_miniref	The FlyBase citation for the publication in which the expression was reported.
Clustering_Analysis_ID	The FlyBase FBlc ID for the dataset representing the clustering analysis.
Clustering_Analysis_Name	The FlyBase name for the dataset representing the clustering analysis.
Source_Tissue_Sex	The sex of the source tissue used for the experiment: male, female or mixed.
Source_Tissue_Stage	The life stage of the source tissue used for the experiment, using only high-level terms: embryonic stage, larval stage, pupal stage, adult stage or mixed.
Source_Tissue_Anatomy	The anatomical region of the source tissue used for the experiment; only "mixed" is shown if many
Cluster_ID	The FlyBase FBlc ID for the dataset representing the cell cluster.
Cluster_Name	The FlyBase name for the dataset representing the cell cluster.
Cluster_Cell_Type_ID	The FlyBase FBbt ID for the cell type represented by the cell cluster.
Cluster_Cell_Type_Name	The FlyBase name for the cell type represented by the cell cluster.
Gene_ID	The FlyBase FBgn ID for the expressed gene.
Gene_Symbol	The FlyBase symbol for the expressed gene (ASCII-format).
Mean_Expression	The average level of expression of the gene across all cells of the cluster in which the gene is detected at all.
Spread	The proportion of cells in the cluster in which the gene is detected.

Physical interaction MITAB file

To download the file, execute the following command.

Physical_interaction_MITAB = Genes.Physical_interaction_MITAB()

Columns Description

Column number	Column heading	General format	FlyBase example	Content description
1	ID(s) Interactor A	database:identifier	flybase:FBgn0002121	The unique Flybase identifier for the first gene of the interacting pair.
2	ID(s) Interactor B	-	-	The unique Flybase identifier for the second gene of the interacting pair.
3	Alt ID(s) Interactor A	database:identifier	flybase:CG2671| entrez gene/locuslink:33156	The alternative gene identifiers currently provided are Flybase annotation IDs (CG#) and NCBI’s Entrez Gene ID separated by “|“
4	Alt ID(s) Interactor B	-	-	-
5	Alias(es) Interactor A	database:name(alias type)	flybase:l(2)gl(gene name)	The official Flybase gene symbol. It is referred to as “gene name” to adhere to the psi-mi ontology.
6	Alias(es) Interactor B	-	-	-
7	Interaction Detection Method(s)	ontology:identifier(method name)	psi-mi:"MI:0006"(anti bait coimmunoprecipitation)	The assay used to detect the interaction, taken from the psi-mi ontology.
8	Publication 1st Author(s)	surname initial(s) (publication year)	Betschinger K. (2003)	The first author and year of the publication where the interaction is described.
9	Publication ID(s)	database:identifier	flybase:FBrf0157155|pubmed:12629552	The unique FlyBase identifier for the publication followed by the unique PubMed identifier (if there is one) separated by “|”.
10	Taxid Interactor A	taxid:identifier	taxid:7227("Drosophila melanogaster")	The NCBI taxonomy identifier for the source organism of the interactor. The vast majority of interactors in FlyBase come from D. melanogaster. There are, however, a few interspecies interactions consisting of a D. melanogaster interactor and an interactor of a different species.
11	Taxid Interactor B	-	-	-
12	Interaction Type(s)	ontology:identifier(interaction type)	psi-mi:"MI:0915"(physical association)	Taken from the psi-mi ontology. Most often “physical association” for FlyBase.
13	Source Database(s)	ontology:identifier(database name)	psi-mi:"MI:0478"(flybase)	All interactions are curated by FlyBase.
14	Interaction Identifier(s)	database:identifier	flybase:FBrf0157155-13.coIP.WB	The unique FlyBase identifier for this interaction.
15	Confidence Value(s)	-	-	Not applicable
16	Expansion Method(s)	-	-	Not applicable
17	Biological Role(s) Interactor A	-	-	Not applicable
18	Biological Role(s) Interactor B	-	-	Not applicable
19	Experimental Role(s) Interactor A	ontology:identifier(experimental role name)	psi-mi:"MI:0496"(bait)	The role played by the interactor in the experiment. Taken from the psi-mi ontology.
20	Experimental Role(s) Interactor B	-	-	-
21	Type(s) Interactor A	ontology:identifier(interactor type name)	psi-mi:"MI:0326"(protein)	The molecule type. For FlyBase, these are limited to protein or ribonucleic acid. Taken from the psi-mi ontology.
22	Type(s) Interactor B	-	-	-
23	Xref(s) Interactor A	-	-	Not applicable
24	Xref(s) Interactor B	-	-	Not applicable
25	Interaction Xref(s)	database:identifier	flybase:FBig0000000103	Cross references for the interactions. For Flybase, these include an interaction group identifier (FBig) and possibly a collection identifier (FBlc) separated by “|”. All experiments that show an interaction between the products of gene A and gene B are compiled into an A-B interaction group, such that all interactions are associated with an interaction group identified by an FBig number. Interactions identified as part of a large scale study are also associated with the collection identifier, or FBlc number.
26	Annotation(s) Interactor A	topic:text isoform-	comment:a isoform	Information on whether the interaction is specific to a particular interactor isoform.
27	Annotation(s) Interactor B	-	-	-
28	Interaction Annotation(s)	topic:text	comment:Phosphorylated isoforms of @l(2)gl@ are absent when @aPKC@ is knocked down by RNAi.	Describes the source(s) of the interaction participants and includes free text comments about the interaction.
29	Host Organism(s)	-	-	Not applicable
30	Interaction Parameters	-	-	Not applicable
31	Creation Date	-	-	Not applicable
32	Update Date	-	-	Not applicable
33	Checksum Interactor A	-	-	Not applicable
34	Checksum Interactor B	-	-	Not applicable
35	Interaction Checksum	-	-	Not applicable
36	Negative	-	FALSE	All interactions in FlyBase are positive.
37	Feature(s) Interactor A	feature_type:range(text)	sufficient binding region:aa 1-58(N-terminal region)	Describes features of Interactor A such as binding sites, mutations that disrupt the interaction, epitope tags, etc.
38	Feature(s) Interactor B	-	-	-
39	Stoichiometry Interactor A	-	-	Not applicable
40	Stoichiometry Interactor B	-	-	Not applicable
41	Identification Method(s) Participant A	-	-	Not applicable
42	Identification Method(s) Participant B	-	-	Not applicable

Functional complementation table

To download the file, execute the following command.

Functional_complementation = Genes.Functional_complementation()

Columns Description

Column heading	Content Description
Dmel gene (symbol)	Current FlyBase symbol of Dmel gene.
Dmel gene (FBgn)	Current FlyBase identifier (FBgn#) of Dmel gene in column 1.
Functionally complementing ortholog (symbol)	Current FlyBase symbol of a non-Dmel ortholog of the Dmel gene in column 1 where this non-Dmel gene has been show to functionally complement the Dmel gene.
Functionally complementing ortholog (FBgn#)	Current FlyBase identifier (FBgn#) of a non-Dmel ortholog of the Dmel gene in column 1 where this non-Dmel gene has been show to functionally complement the Dmel gene.
Supporting_FBrf	Current FlyBase identifier (FBrf#) of the publication that provides support for the functional complementation statement (the publication that reported the suppression of a mutant phenotype of the Dmel gene by a transgenic construct/mutant allele of the non-Dmel ortholog).

FBgn to DB Accession IDs

To download the file, execute the following command.

FBgn_toDB_Accession_IDs = Genes.FBgn_toDB_Accession_IDs()

Columns Description

Column heading	Content Description
gene_symbol	Current symbol of gene.
organism_abbreviation	Abbreviation (from the Species Abbreviations list) indicating the species of origin of the gene.
primary_FBgn#	Current FlyBase identifier (FBgn#) of gene.
nucleotide_accession	EMBL/GenBank/DDBJ nucleotide accession associated with the gene.
na_based_protein_accession	EMBL/GenBank/DDBJ protein accession associated with the gene and the nucleotide accession in the preceeding 'nucleotide_accession' column
UniprotKB/Swiss-Prot/TrEMBL_accession	UniProtKB/SwissProt/TrEMBL protein accession associated with the gene.
EntrezGene_ID	NCBI Entrez ID associated with the gene.
RefSeq_transcripts	NCBI RefSeq transcript accession associated with the gene.
RefSeq_proteins	NCBI RefSeq protein accession associated with the gene and the transcript accession in the preceeding 'RefSeq_transcripts' column.

FBgn to Annotation ID

To download the file, execute the following command.

FBgn_toAnnotation_ID = Genes.FBgn_toAnnotation_ID()

Columns Description

Column heading	Content Description
gene_symbol	Current symbol of gene.
organism_abbreviation	Abbreviation (from the Species Abbreviations list) indicating the species of origin of the gene.
primary_FBgn#	Current FlyBase identifier (FBgn#) of gene.
secondary_FBgn#(s)	Secondary FlyBase identifier(s) (FBgn#) associated with the gene (comma separated values).
annotation_ID	Current annotation identifier associated with the gene.
secondary_annotation_ID(s)	Secondary annotation identifier(s) associated with the gene (comma separated values).

FBgn to GLEANR IDs

To download the file, execute the following command.

FBgn_toGLEANR_IDs = Genes.FBgn_toGLEANR_IDs()

Columns Description

Column heading	Content Description
organism_abbreviation	Abbreviation (from the Species Abbreviations list) indicating the species of origin of the gene.
gene_symbol	Current FlyBase gene symbol.
primary_FBgn#	Current FlyBase identifier (FBgn#) of the gene.
GLEANR_ID	GLEANR identifier assigned by the AAA Consortium.

FBgn to FBtr to FBpp IDs

To download the file, execute the following command.

FBgn_to_FBtr_to_FBpp = Genes.FBgn_to_FBtr_to_FBpp()

Columns Description

Column heading	Content Description
FlyBase_FBgn	Current FlyBase identifier (FBgn#) of the gene.
FlyBase_FBtr	Current FlyBase identifier (FBtr#) of a transcript encoded by the gene listed in the preceeding 'FlyBase_FBgn' column.
FlyBase_FBpp	Current FlyBase identifier (FBpp#) of a polypeptide encoded by the transcript listed in the preceeding 'FlyBase_FBtr' column, where this is relevant.

FBgn to FBtr to FBpp IDs (expanded)

To download the file, execute the following command.

FBgn_to_FBtr_to_FBpp_exp = Genes.FBgn_to_FBtr_to_FBpp_expanded()

Columns Description

Column heading	Content Description
organism	Abbreviation (from the Species Abbreviations list) indicating the species of origin of the gene.
gene_type	The type of gene, represented by a Sequence Ontology term.
gene_ID	Current "FBgn" identifier of gene.
gene_symbol	Current symbol of the gene.
gene_fullname	Current full name of the gene.
annotation_ID	Current FlyBase annotation identifier of the gene.
transcript_type	The type of transcript, represented by a Sequence Ontology term.
transcript_ID	Current FlyBase annotation identifier of the transcript.
transcript_symbol	Current symbol of the transcript.
polypeptide_ID	Current FlyBase annotation identifier of the polypeptide.
polypeptide_symbol	Current symbol of the polypeptide.

FBgn exons to Affy1

To download the file, execute the following command.

FBgn_exons2affy1 = Genes.FBgn_exons2affy1()

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

The first column of a line it is the FBgn ID, and the second one is the Affy1 ID that overlaps with an exon of the gene.

FBgn exons to Affy2

To download the file, execute the following command.

FBgn_exons2affy2 = Genes.FBgn_exons2affy2()

Similar to the Affy1 but with Affy2.

Genes Sequence Ontology (SO) data

To download the file, execute the following command.

Genes_Sequence_Ontology = Genes.Genes_Sequence_Ontology()

Columns Description

Column heading	Content Description
gene_primary_id	The unique FlyBase gene ID for this gene.
gene_symbol	The official FlyBase symbol for this gene.
so_term_name	The SO term name.
so_term_id	The SO term primary identifier.

Genes map table

To download the file, execute the following command.

Genes_map = Genes.Genes_map()

Columns Description

Column heading	Content Description
organism_abbreviation	Abbreviation (from the Species Abbreviations list) indicating the species of origin of the gene.
current_symbol	Current FlyBase gene symbol.
primary_FBid	Current FlyBase identifier (FBgn#) of gene.
recombination_loc	Recombination map location.
cytogenetic_loc	Cytogenetic location.
sequence_loc	Genomic location.

Best gene summaries

To download the file, execute the following command.

Best_gene_summaries = Genes.Best_gene_summaries()

Columns Description

Column heading	Content Description
FBgn_ID	Current FlyBase identifier number for the gene.
Gene_Symbol	Current FlyBase symbol of the gene.
Summary_Source	The source of the gene summary.
Summary	The gene summary text.

Automated gene summaries

To download the file, execute the following command.

Automated_gene_summaries = Genes.Automated_gene_summaries()

Columns Description

Column heading	Content Description
FlyBase ID.	The Valid FlyBase identifier number for the gene.
Summary	The gene summary as a string of plain text.

Gene Snapshots

To download the file, execute the following command.

Gene_Snapshots = Genes.Gene_Snapshots()

Columns Description

Column heading	Content Description
FBgn_ID	Current FlyBase identifier number for the gene.
GeneSymbol	Current FlyBase symbol of the gene.
GeneName	Current FlyBase name of the gene.
datestamp	Date on which the information was last reviewed.
gene_snapshot_text	Gene snapshot information for the gene. Cases that are in progress or are deemed to have insufficient data to summarize are stated as such

Unique protein isoforms

To download the file, execute the following command.

Unique_protein_isoforms = Genes.Unique_protein_isoforms()

Columns Description

Column heading	Content Description
FBgn	Current FlyBase identifier (FBgn#) of the gene.
FB_gene_symbol	Current FlyBase gene symbol of the gene.
representative_protein	Current FlyBase protein symbol of the representative protein isoform.
identical_protein(s)	Current FlyBase protein symbol(s) of identical protein isoforms.

Non-coding RNAs

To download the file, execute the following command.

Noncoding_RNAs = Genes.Noncoding_RNAs()

This file reports all ncRNAs with gene models supported by FlyBase in JSON format, as submitted to RNAcentral. Pseudogenes are excluded. In addition to the symbols and IDs for ncRNAs, this file also includes their associated gene, genomic location, sequence, Sequence Ontology classification, etc.

Enzyme data

To download the file, execute the following command.

Enzyme = Genes.Enzyme()

Columns Description

Column heading	Content Description
group_id	FlyBase gene group (FBgg) ID of the relevant terminal group within the ENZYMES (FBgg0001715) hierarchy (only terminal groups contain members).
group_name	FlyBase gene group (FBgg) name of relevant terminal group within the ENZYMES (FBgg0001715) hierarchy (only terminal groups contain members).
group_GO_ID	The GO molecular function term ID on the given gene group. Multiple entries are separated with a pipe.
group_GO_name	The GO molecular function term name on the given gene group. Multiple entries are separated with a pipe.
group_EC_number	The EC number on the given gene group, if present. (This is computed, corresponding to the EC cross-reference on the GO molecular function term.)
group_EC_name	The EC name on the given gene group, if present. (This is computed, corresponding to the EC cross-reference on the GO molecular function term.)
gene_id	The current FlyBase gene ID (FBgn) of the gene.
gene_symbol	The current FlyBase symbol of the gene.
gene_name	The current FlyBase name of the gene.
gene_EC_number	The EC number(s) associated with the gene, if present. Multiple entries are separated with a pipe. (This is computed, corresponding to the EC cross-reference(s) on any positive GO molecular function term(s) annotated to the gene.)
gene_EC_name	The EC name(s) associated with the gene, if present. Multiple entries are separated with a pipe. (This is computed, corresponding to the EC cross-reference(s) on any positive GO molecular function term(s) annotated to the gene.)

Gene Ontology annotation files

To facilitate its usage, it is suggested to access the data using the following command.

GOAnn = FBD.GOAnn

Then, enter the specific method according to the desired data

Gene Association File - GAF

Columns Description

Column heading	Content Description
DB	The database contributing the gene_association file FB File: always "FB" for gene_association.fb.
DB Object ID	A unique identifier in the database for the item being annotated. FB File: This is always the primary FlyBase identifier number for a Drosophila gene. Example: FBgn0000490
DB Object Symbol	A (unique and valid) symbol to which the DB Object ID is matched. FB File: This is always the valid gene symbol for a Drosophila gene. Example: dpp
Qualifier	For each GO annotation, one of the following as gene product to term relations are used: 'acts_upstream_of', 'acts_upstream_of_negative_effect', 'acts_upstream_of_positive_effect', 'colocalizes_with', 'contributes_to', 'enables', 'involved_in', 'is_active_in', 'located_in', 'part_of'. This column may also contain the 'NOT' qualifier, separated by a pipe (“|”) from the gene product to term relation, which makes the annotation statement a negation.
GO ID	The unique GO identifier for the GO term attributed to the DB_Object_ID. Example: GO:0005160
DB:Reference	The unique identifier for the reference to which the GO annotation is attributed. FB File: Each FlyBase reference including published literature, conference abstracts, personal communications, sequence records and computer files has a unique 7 digit identifier (an FBrf). Where this reference is a published paper with a PubMed identifier, the PubMed ID is also listed in column 6, separated from the FBrf with a pipe (“|”). Example: FB:FBrf0136863|PMID:11432817
Evidence	The evidence code for the GO annotation; one of IMP, IGI, IPI, ISS, IDA, IEP, IEA, TAS, NAS, ND, IC, RCA, HDA, HMP, HGI, HEP, IBA
With (or) From	FB File: This column contains the identifier for annotations where the evidence code is IGI, IPI, ISS, IEA or IC. For IGI the database gene symbol and identifier is listed. For ISS and IPI the identifier can be a gene symbol and identifier, or a sequence (protein or nucleic acid) identifier. For IC, the GO identifier of the term used as the basis of a curator inference is given. IGI example: FLYBASE:rpr; FB:FBgn0011706, ISS example: UniProt:P35569, ISS example: EMBL:AF064523, ISS example: SGD_LOCUS:COP1; SGD:S0002304, IC example: GO:0045298
Aspect	Which ontology the GO term belongs to: Function ( F ), Process ( P ) or Component ( C ). Example: P
DB Object Name	FB File: The full name of the FlyBase gene. Example: decapentaplegic Where a FlyBase gene has no full name (eg Pten), this field is left blank.
DB Object Synonym	Alternative names by which the database object is known. FB File: Multiple synonyms of a FlyBase gene are separated by a pipe (“|”). Example: M(2)LS1|shortvein|Dm-DPP|dpp|Dpp|DPP|CG9885|TGF-beta|TGF-&bgr|TGF-b|Hin-d|l(2)10638|shv|DPP-C|ho|M(2)23AB|blk|l(2)22Fa|l(2)k17036|Tg|TGF&bgr
DB Object Type	The type of object being annotated. Always a gene for FlyBase data. FB file: always "gene" for gene_association.fb.
Taxon	The taxonomic identifier of the species encoding the gene product Example: taxon:7227
Date	The date of last annotation update, in the format 'YYYYMMDD'. At present this date is the same for all annotations and corresponds to the date of the latest FlyBase update; we are in the process of changing our system so that dates more accurately reflect the date the annotation is made. Example: 20040821
Assigned by	The source of the GO annotation.

Gene groups

To facilitate its usage, it is suggested to access the data using the following command.

Gene_groups = FBD.Gene_groups

Then, enter the specific method according to the desired data

Gene group

To download the file, execute the following command.

Gene_groups_data = Gene_groups.Gene_group() 

Columns Description

Column heading	Content Description
FB_group_id	Current FlyBase identifier (FBgg##) of Gene Group.
FB_group_symbol	Current FlyBase symbol of Gene Group.
FB_group_name	Current FlyBase full name of Gene Group.
Parent_FB_group_id	Current FlyBase identifier (FBgg##) of parent of given Gene Group (if relevant).
Parent_FB_group_symbol	Current FlyBase symbol of parent of given Gene Group (if relevant).
Group_member_FB_gene_id	Current FlyBase identifier (FBgn##) of member gene (if terminal group).
Group_member_FB_gene_symbol	Current FlyBase symbol of member gene (if terminal group).

Gene groups with HGNC IDs

To download the file, execute the following command.

Gene_groups_HGNC= Gene_groups.Gene_groups_HGNC()

Columns Description

Column heading	Content Description
FB_group_id	Current FlyBase identifier (FBgg##) of Gene Group.
FB_group_symbol	Current FlyBase symbol of Gene Group.
FB_group_name	Current FlyBase full name of Gene Group.
HGNC_family_ID	HGNC ID of equivalent human 'gene family'.

Pathway group

To download the file, execute the following command.

Pathway_group = Gene_groups.Pathway_group()

Columns Description

Column heading	Content Description
FB_group_id	Current FlyBase identifier (FBgg##) of Pathway Gene Group.
FB_group_symbol	Current FlyBase symbol of Pathway Gene Group.
FB_group_name	Current FlyBase full name of Pathway Gene Group.
Parent_FB_group_id	Current FlyBase identifier (FBgg##) of parent of given Pathway Gene Group (if relevant).
Parent_FB_group_symbol	Current FlyBase symbol of parent of given Pathway Gene Group (if relevant).
Group_member_FB_gene_id	Current FlyBase identifier (FBgn##) of member gene (if terminal group).
Group_member_FB_gene_symbol	Current FlyBase symbol of member gene (if terminal group).

Alleles and Stocks

To facilitate its usage, it is suggested to access the data using the following command.

Alleles_Stocks = FBD.Alleles_Stocks

Then, enter the specific method according to the desired data

Stock data

To download the file, execute the following command.

Stock = Alleles_Stocks.Stock()

Columns Description

Column heading	Content Description	Example
FBst	The unique identifier assigned to this stock by FlyBase.	FBst0000002
collection_short_name	A short name for the stock collection that holds the stock.	Bloomington
stock_type_cv	The controlled vocabulary term and unique identifier that describe the state of the stock.	living stock ; FBsv:0000002
species	Abbreviation (from the Species Abbreviations list) indicating the species of the stock.	Dmel
FB_genotype	Genetic components of the stock corresponding to alleles, aberrations, balancers, or insertions in FlyBase. May be empty.	w[*]; betaTub60D[2] Kr[If-1]/CyO
description	Genetic components of the stock as provided to FlyBase by the collection that holds the stock.	FlyTrap: ZCL1796 III
stock_number	The stock identifier provided to FlyBase by the collection that holds the stock. May be empty.	110818

Genetic interactions

To download the file, execute the following command.

Genetic_interactions = Alleles_Stocks.Allele_genetic_interactions()

Columns Description

Column heading	Content Description
allele_symbol	Current FlyBase allele symbol.
allele_FBal#	Current FlyBase identifier (FBal#) of allele.
interaction	Interaction information associated with allele.
FBrf#	Current FlyBase identifer (FBrf#) of publication from which data came.

Phenotypic data

To download the file, execute the following command.

Phenotypic_data = Alleles_Stocks.Phenotypic()

Columns Description

Column heading	Content Description
genotype_symbols	Current FlyBase symbol(s) of the components that make up the genotype.
genotype_FBids	Current FlyBase identifier(s) of the components that make up the genotype.
phenotype_name	Phenotypic name associated with the genotype.
phenotype_id	Phenotypic identifier associated with the genotype.
qualifier_names	Qualifier name(s) associated with phenotypic data for genotype.
qualifier_ids	Qualifier identifier(s) associated with phenotypic data for genotype.
reference	Current FlyBase identifer (FBrf#) of publication from which data came.

Alleles to Genes

To download the file, execute the following command.

Alleles_toGenes = Alleles_Stocks.FBal_to_FBgn()

Columns Description

Column heading	Content Description
AlleleID	Current FlyBase identifier (FBal#) of the allele.
AlleleSymbol	Current symbol of the allele.
GeneID	Current FlyBase identifier (FBgn#) of the gene.
GeneSymbol	Current symbol of the gene.

Homologs

To facilitate its usage, it is suggested to access the data using the following command.

Homologs = FBD.Homologs

Then, enter the specific method according to the desired data

Drosophila Paralogs

To download the file, execute the following command.

Dmel_Paralog = Homologs.Drosophila_Paralogs()

Columns Description

Column heading	Content Description
FBgn_ID	Current FlyBase identifier (FBgn#) of the D. melanogaster gene.
GeneSymbol	Current FlyBase gene symbol of the D. melanogaster gene.
Arm/Scaffold	Arm upon which the D. melanogaster gene is localized.
Location	Location of D. melanogaster gene on the arm.
Strand	Strand of D. melanogaster gene ('1' indicates the positive strand, '-1' indicates the negative strand).
Paralog_FBgn_ID	Current FlyBase identifier (FBgn#) of the paralogous gene.
Paralog_GeneSymbol	Current FlyBase gene symbol of the paralogous gene.
Paralog_Arm/Scaffold	Arm upon which the paralogous gene is localized.
Paralog_Location	Location of paralogous gene on the arm.
Paralog_Strand	Strand of paralogous gene ('1' indicates the positive strand, '-1' indicates the negative strand).
DIOPT_score	DIOPT 'score' for the paralog call (i.e. the number of individual algorithms that support the call).

Human Orthologs

To download the file, execute the following command.

Hman_Orthologs = Homologs.Human_Orthologs()

Columns Description

Column heading	Content Description
Dmel_gene_ID	Current FlyBase identifier (FBgn#) of the D. melanogaster gene.
Dmel_gene_symbol	Current FlyBase gene symbol of the D. melanogaster gene.
Human_gene_HGNC_ID	HGNC ID of orthologous human gene.
Human_gene_OMIM_ID	OMIM ID of orthologous human gene.
Human_gene_symbol	HGNC gene symbol of orthologous human gene.
DIOPT_score	DIOPT 'score' for orthology call (i.e. the number of individual algorithms that support the call).
OMIM_Phenotype_IDs	OMIM Phenotype ID of orthologous human gene (comma separated values).
OMIM_Phenotype_IDs[name]	OMIM Phenotype ID of orthologous human gene (with the corresponding OMIM name in square brackets).

Human disease

To facilitate its usage, it is suggested to access the data using the following command.

Human_disease = FBD.Human_disease

Human disease model data

To download the file, execute the following command.

Human_disease_model = Human_disease.Disease_model_annotations()

Columns Description

Column heading	Content Description
FBgn ID	Current FlyBase identifier (FBgn#) of the gene associated with the allele of an experimental annotation, or the D. melanogaster ortholog of a human gene associated with a disease in OMIM.
Gene symbol	Current FlyBase symbol of the gene in column 1.
HGNC ID	HGNC ID of the gene identified in column 1 where it is a human gene (experimental-based annotations only).
DO qualifier	Type of association between the object of annotation and the disease - one of 'model of', 'ameliorates', 'exacerbates', 'DOES NOT model', 'DOES NOT ameliorate' or 'DOES NOT exacerbate'.
DO ID	Disease Ontology (DO) ID.
DO term	Disease Ontology (DO) term.
Allele used in model (FBal ID)	Current FlyBase identifier (FBal#) of allele (experimental-based annotations only).
Allele used in model (symbol)	Current FlyBase symbol of allele (experimental-based annotations only).
Based on orthology with (HGNC ID)	HGNC ID of the human ortholog used for annotations based on orthology to human disease genes.
Based on orthology with (symbol)	HGNC gene symbol of the human ortholog used for annotations based on orthology to human disease genes.
Evidence/interacting alleles	Evidence code, with interacting allele(s) where appropriate. For experimental-based annotations, the evidence code is one of: 'inferred from mutant phenotype', 'in combination with', 'modeled by', 'is ameliorated by', 'is exacerbated by', 'is NOT ameliorated by' or 'is NOT exacerbated by'. Interacting alleles are give as 'FLYBASE:<allele_symbol>; FB:<FBal_ID>', with multiple alleles separated by a comma. For orthology-based annotations, the evidence code is 'inferred from electronic annotation'.
Reference (FBrf ID)	Current FlyBase identifier (FBrf#) of the source publication.

Human orthologs

To download the file, execute the following command.

Hman_Orthologs = Human_disease.Human_Orthologs()

This is identical to the file of the same name listed under the 'Orthologs' section above.

Organisms

Species list

To download the file, execute the following command.

Species = FBD.Organisms.Species_list()

Columns Description

Column heading	Content Description
Genus	The genus designation of the organism.
Species name	The species designation of the organism.
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 no individual report page exists for that species in FlyBase.
Common name	The NCBI Taxonomy Database common name of the organism. This column may be blank.
Ncbi-taxon-id	The NCBI Taxonomy Database Taxon ID for the organism. This column may be blank.
drosophilid	If the species is from the family Drosophilidae, this column is filled in with 'y'.

Ontology Terms

To facilitate its usage, it is suggested to access the data using the following command.

Ontology = FBD.Ontology_Terms

Fly anatomy

FBbt = Ontology.FBbt()

Fly development

FBdv = Ontology.FBdv()

Flybase controlled vocabulary

FBcv = Ontology.FBcv()

Stock ontology

FBsv = Ontology.FBsv()

Gene ontology

GO = Ontology.G0()

Image ontology

FBbi= Ontology.FBbi()

Human disease ontology

DO = Ontology.DO()

Insertions

To facilitate its usage, it is suggested to access the data using the following command.

Insertions = FBD.Insertions

Map data for insertions

To download the file, execute the following command.

map_Insertions = Insertions.Map_insertions()

Columns Description

Column heading	Content Description
insertion_symbol	Current symbol of insertion.
FBti#	Current FlyBase identifier (FBti#) of insertion.
genomic_location	Genomic location of insertion.
range	Range (t/f) indicates whether genomic location is range or single base
orientation	Orientation (1/0) indicates orientation of insertion on chromosome.
estimated_cytogenetic_location	Estimated cytogenetic location based on correlation of genomic location and estimated genomic location of cytological bands.
observed_cytogenetic_location	Observed cytogenetic location reported in the literature.

Frequently-used GAL4 drivers

To download the file, execute the following command.

Gal4 = Insertions.GAL4_drivers()

This file reports a list of all GAL4 drivers that have been curated to at least 21 references and/or are among 150 most frequently requested GAL4 stocks from the Bloomington Drosophila Stock Center, in JSON format. In addition to the symbols and IDs for Scer\GAL4 alleles, this file also includes their associated transposon or insertion, associated gene, expression pattern in controlled vocabulary stage and anatomy terms, stocks, and publications, all with IDs, as well as free text expression pattern descriptions. This file, except for publications and stocks, is also available in TSV format here.

Clones

To facilitate its usage, it is suggested to access the data using the following command.

Clones = FBD.Clones

cDNAs: FBcl to acc. ID

To download the file, execute the following command.

c_cDNAs = Clones.cDNA_clone_data()

Columns Description

Column heading	Content Description
FBcl#	Current FlyBase identifier (FBcl#) of cDNA clone.
organism_abbreviation	Abbreviation (from the Species
clone_name	Clone name.
dataset_metadata_name	Name of dataset associated with clone.
cDNA_accession(s)	EMBL/GenBank/DDBJ cDNA accession number.
EST_accession(s)	EMBL/GenBank/DDBJ EST accession number.

Genomic: FBcl to acc. ID

To download the file, execute the following command.

c_genomic = Clones.genomic_clone_data()

Columns Description

Column heading	Content Description
FBcl#	Current FlyBase identifier (FBcl#) of genomic clone.
organism_abbreviation	Abbreviation (from the Species Abbreviations list) indicating the species of origin of the clone.
clone_name	Clone name.
accession	EMBL/GenBank/DDBJ cDNA accession number.

References

FlyBase FBrf to PubMed ID to PMCID to DOI

To download the file, execute the following command.

References = FBD.References.FBrf_PMid_PMCid_doi()

Columns Description

Column heading	Content Description
FBrf	The unique FlyBase ID for this publication.
PMID	The unique PubMed ID for this publication.
PMCID	The unique PubMed Central ID for this publication, if applicable.
DOI	The digital object identifier assigned to the publication.
pub_type	The publication type (for example, paper, review, erratum, abstract, book, etc.)
miniref	A short citation listing the first author, year of publication, journal, volume, issue and page numbers.
pmid_added	The FlyBase release in which the publication was first incorporated into the FlyBase bibliography. Note: as this report first generated for fb_2012_01 release, all publications associated with a Pub Med ID prior to this release have pmid_added = fb_2011_10.

Autor:

Javiera Quiroz, email.