FlyBase:Dataset-Collection Report

Last Updated: 21 December 2017

The Dataset Report provides information on large datasets and reagent collections. These are represented as distinct but related components, each a distinct FlyBase entity with its own tailored report: the "biosample" (biological source material), the "assay" (generation of raw data from a biosample) and the "result" (analyses of data generated by an assay, or other results). A "project" report groups together related reagent collections, or related datasets from a single study. So, there are slightly different report types for each dataset component, differing in content and overall organization. Some information is specific to certain report types, other information may found in most/all report types but sometimes shown under different sections. The field-by-field documentation here indicates the report type to which the field applies.

General Information

Field	Report Types	Description
Name	all	The name that FlyBase uses for this dataset.
<dataset> type	all	For a given dataset component, the type of dataset or reagent collection: e.g., in a reagent report, the "Reagent type' might be indicated as "cDNA library".
(Parent) Project	all	The project to which a biosample, assay, reagent collection or result belongs to. For a project, the umbrella or "Parent" project.
Title	all	A short description of the data or reagents represented by the dataset/collection.
Status	result	The status is indicated as either "Current" or, for a deprecated result, the result(s) that replace(s) this one: e.g., DPiM-1.
Accessions	all	A listing of external database IDs (with links to those external accessions).
Species	all	The organism from which the biological material or data were derived.
FlyBase ID	all	The FlyBase identifier number of the dataset, used to uniquely identify the dataset in the database.
Generated by	all	The lab or group that generated the data or reagents, sometimes linked out to their web page.

Overview

Field	Report Types	Description
Description	project, reagent	A longer description of the study, or for a reagent collection, the type of reagent and its intended uses.
Available from	reagent	A resource where the reagents described can be obtained, sometimes linked out to their web page.
Project attributes	project	A list of controlled vocabulary terms that describe the project: e.g., "developmental stage study" or "tissue type study".
Biosample type	project	The types of biosamples generated in a given project.
Assay type	project	The types of assays performed in a given project.
Reagent type	project	The types of reagent collections generated in a given project.
Result type	project	The types of results obtained in a given project.
Key genes	project	Key genes that were experimentally manipulated in treatment samples, as well an indication of how they were manipulated.
GO terms	project	GO terms representing biological processes or molecular functions studied in the project.
SO terms	project	SO terms representing sequence types studied in the project.

Details

Field	Report Types	Description
Sample preparation	project	Description of key experimental details in the growth, treatment and isolation of the source biological material. Information reported here is limited to what is common to all biosamples in a given project. See individual "biosample" reports for more details.
Protocol	project	Description of key experimental details in the processing of biomolecules (post-cell lysis). Information reported here is limited to what is common to all assays or reagent collections in a given project. See individual "assay" or "reagent" reports for more details.
Mode of assay	project	Description of key experimental details in the techniques used to assay the processed biological material. Information reported here is limited to what is common to all assays or reagent collections in a given project. See individual "assay" or "reagent" reports for more details.
Data analysis	project	Description of key experimental details in the processing of raw data, including mapping data to genes/genomes, data normalization, and methods used to identify peaks, clusters, etc. Information reported here is limited to what is common to all results in a given project. See individual "result" reports for more details.
Comments	project	Additional free text comments.
Files	project	Downloadable files (with the file format, size and short notes in parentheses).

Genetic Background

Field	Report Types	Description
Strain	biosample	The fly strain of the source biological material.
Genotype	biosample	The genotype of the source biological material.
Key genes	biosample	Key genes that were experimentally manipulated in treatment samples, as well an indication of how they were manipulated.

Source Material

Stage	Tissue/Position	Reference
The developmental stage used as the source of biological material.	The tissue used as the source of biological material	The reference from which the sample information was obtained.

Field	Report Types	Description
Cell line	biosample	The cell line used as the source of biological material.
Other tissues studied	biosample	Tissues perturbed in the animal specimen, which may be distinct from the actual tissue collected: e.g., one may perturb "mushroom body" but collect "whole head".
Other species studied	biosample	Indicates species used as treatments (infection, parasitization, nutrition), or for microbiome studies, the host species.

Biosample Details

Field	Report Types	Description
Methods	biosample	Terms that describe the methods used to treat and isolate the biological material.
Reagents	biosample	Reagents used to treat and isolate the biological material, with links to relevant FlyBase reports. This includes reagent collections, alleles, transgenes, etc.
Sample preparation	biosample	Description of key experimental details in the growth, treatment and isolation of the source biological material.
Comments	biosample	Additional free text comments.
Files	biosample	Downloadable files (with the file format, size and short notes in parentheses).

Biosample Source

Field	Report Types	Description
Strain	assay, reagent, result	The fly strain of the source biological material.
Stage	assay, reagent, result	General stages represented by the biosample(s) used as input for the assay, reagent or result.
Sex	assay, reagent, result	The sex (as defined by sex chromosome complement) of the biosample(s) used as input for the assay, reagent or result.
Tissue isolated	assay, reagent, result	The tissue collected in the biosample(s) used as input for the assay, reagent or result.
Other tissues studied	assay, reagent, result	Tissues perturbed in the biosample(s) used as input for the assay, reagent or result, which may be distinct from the actual tissue collected: e.g., one may perturb "mushroom body" but collect "whole head".
Cell component	assay, reagent, result	The subcellular compartments collected in the biosample(s) used as input for the assay, reagent or result.
Cell line	assay, reagent, result	The cell line used as the source of biological material.
Key genes	assay, reagent, result	Key genes that were experimentally manipulated in treatment samples, as well an indication of how they were manipulated.
Methods	assay, reagent, result	Terms that describe the methods used to treat and isolate the biosample(s) used as input for the assay, reagent or result.
Sample preparation	assay, reagent, result	Description of key experimental details in the growth, treatment and isolation of biosample(s) used as input for the assay, reagent or result.
Biosamples used	assay, reagent	Symbol, type and title for biosamples processed in an assay or reagent collection.

Assay Details

TABLE TEMPLATE:

Field	Report Types	Description
Methods	assay, reagent	Controlled terms representing the methods used in an assay, or in the construction of a reagent collection.
Key genes	assay	Key genes representing experimental conditions in the assay, along with their role in the assay: e.g., Ubx (bait protein).
Reagents	assay, reagent	A list of molecular constructs, alleles, transgenes and reagent collections used in the assay, or in building the reagent collection; links to these reagents are provided.
Protocol	assay, reagent	Description of key experimental details in the processing of biomolecules (post-cell lysis).
Mode of assay	assay, reagent	Description of key experimental details in the techniques used to assay the processed biological material.
Data analysis	reagent	Any data analysis used in the construction of the reagent collection.
Comments	assay, reagent	Additional comments.

Associated Data

Field	Report Types	Description
Size	assay, reagent, result	A free text comment describing the size of the dataset.
Associated features	assay, reagent, result	Reports the type and number of features associated with the dataset, with options to download the list or view the features in a FlyBase hitlist.
Associated strains	reagent	Reports the number of strains associated with the reagent collection, with options to download the list or view the strains in a FlyBase hitlist.
Associated cell lines	reagent	Reports the number of cell lines associated with the reagent collection, with options to download the list or view the cell lines in a FlyBase hitlist.
Associated interactions	result	Reports the number of interactions associated with the result.
Files	project	Downloadable files (with the file format, size and short notes in parentheses).

Related Datasets

Field	Report Types	Description
Parent projects	all	Project to which the report subject belongs.
Component projects	project	Sub-projects for a given project.
Biosamples generated	project	Biosamples generated as part of a project.
Biosamples reanalyzed	project	Biosamples generated by other projects, for which derived raw data was reanalyzed in this project.
Raw data generated	project	Assays that generated raw data in this project.
Raw data reanalyzed	project	Assays from other projects for which raw data was reanalyzed in this project.
Reagent collections	project	Reagent collections generated by this project.
Processed data generated	project	Processed data (results) generated by this project.
Processed data reanalyzed	project	Processed data (results) generated by other projects that was re-analyzed by this project.
Raw data generated from this biosample	biosample	Assays generating raw data from this biosample.
Reagent collections generated from this biosample	biosample	Reagent collections generated from this biosample.
Processed data generated from this biosample	biosample	Processed data (results) generated from raw data obtained for this biosample.
Processed data generated from this assay	assay, reagent	Processed data (results) obtained by analysis of raw data generated by this assay.
Other assays (via shared biosamples)	assay, reagent	Other assays of the same source biosample as this assay.
Parent results	result	For component clusters, the clustering analysis result to which they belong.
Component results	result	For a clustering analysis result, the component clusters.
Further analyses of these result	result	Other processed data (results) that used this result as input data.

Synonyms & Secondary IDs

Reported As

Field	Report Types	Description
Symbol Synonym	all	A list of symbols that have been used in the literature, or by FlyBase, to describe the dataset.

Secondary FlyBase IDs

For all dataset report types, a list of Secondary FlyBase identifier numbers of the dataset. If a dataset has a secondary identifier number, it generally indicates that at some point it has been merged with or split from other entries in the database.

References

For all dataset report types, a list of references to which all data in the report is attributed. The number in the section title indicates the total number of references. The left margin allows filtering of references by reference type.