FlyBase:Dataset-Collection Report

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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

In biosample reports, detailed compound statements describe the tissue that was collected.

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

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.

Data Analyzed

Field Report Types Description
Assay result The assay types generating the raw data used as input for this result.
Assay methods result The assay methods used to generate the raw data used as input for this result.
Key genes result Genes representing experimental conditions in the assays used to generate the raw data used as input for this result.
Protocol result Description of key experimental details in the processing of biomolecules (post-cell lysis) used to generate the raw data used as input for this result.
Mode of assay result Description of key experimental details in the techniques used to assay the processed biological material and generate the raw data used as input for this result.
Raw data analyzed result The symbol, type and title of assays providing raw data used as input for this result.
Processed data analyzed result The symbol, type and title of results providing processed data used as input for this result.

Analysis

Field Report Types Description
Attributes result Controlled terms describing aspects of the result, including analysis techniques and output data types.
Reference Genome result The genome assembly serving as a reference for the data associated with this result.
Reference Annotation result The gene model annotation set serving as a reference for the data associated with this result.
Data analysis result 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.
Comments result Additional comments on the processed data represented in this result report.

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.