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.
|
| Data Provider |
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
|
| Methods |
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).
|
| Additional Information |
result |
|
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.