Release Pipeline: Difference between revisions

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* Groups wishing to contribute their annotations to GO should have their group added into the '''GO groups''' metadata: <br /> https://github.com/geneontology/go-site/blob/master/metadata/groups.yaml
* Groups wishing to contribute their annotations to GO should have their group added into the '''GO groups''' metadata: <br /> https://github.com/geneontology/go-site/blob/master/metadata/groups.yaml
* The location of the annotations to be uploaded by GO should be: <br /> '''TODO'''
* The location of the annotations to be uploaded by GO should be: <br /> '''TODO'''


== Data sources ==
== Data sources ==

Revision as of 17:40, 27 August 2018

August 2018: This documentation is currently a work in progress.

Overview

The information below is intended for GOC members who are providers of annotations. It describes how GOC processes annotations, that can be viewed at locations like AmiGO, downloaded from our sites, and queried via the SPARQL endpoint.

Submitting GO Data

Data sources

  • Primary annotations by GOC contributing groups
    • Annotation files produced by GOC members are accessed via the URL or address provided by each group's datasets metadata file, in the source field. The files must be made publicly available via HTTP or FTP to be pulled in by GO. Important note: the source URL must resolve to the latest annotation file produced by the submitting group, since that link is used directly when fetching the data.
    • More information about the format of the datasets metadata file can be found in the metadata schema.yaml file.
  • PAINT annotations: https://github.com/geneontology/go-site/tree/master/metadata/datasets datasets metadata file

Data from these sources are merged, checked as described in the Annotation QA/QC checks section, and processed to publish exported files.

Data processing: annotation merging

Merging of annotations integrates data from the upstream GAF and PAINT annotations (if available). After QC, the annotations passing the filters are included in the final publish files.

Annotation QA/QC checks

  • A number of checks are ran to ensure the integrity of the data. Checks include: data format, validity of identifiers, and a number of annotation rules. There are three types of checks:
    • filter: Violations of the rule lead to the filtering out of annotations not conforming.
    • repair: Violations of the rule lead to a replacement of the incorrect value by the correct value (for example, annotations to alternate identifiers are changed to the main id).
    • report: Violations of the rule are reported in the annotation reports.
  • The checks are documented here: https://github.com/geneontology/go-site/blob/master/metadata/rules/README.md.
  • Errors are reported in Annotation Reports.

Data publishing and access

Once the upstream files have been loaded, checked, and merged, GAFs, GPADs, GPIs, and other files are produced and published. Data produced by each release can be accessed at the URLs below:

Release schedule and content

The GO Consortium (GOC) is now publicly releasing data on a monthly basis. The public release pipeline runs monthly, starting at midnight (12am PDT) on the 1st of each month (or as close as can be obtained if there are failures). Releases contain:


Published Files and Reports

  • The annotation release pipeline generates many different products, including primary products such as annotation and GPI files and reports (such as error reports) and inferred annotations (for providing feedback to GOC contributing groups like MODs and UniProt).
  • Below is more detailed information about what files are generated during a release, using the citable URLs from the 2018-07-02 release as an example. A typical directory, for example http://release.geneontology.org/2018-07-02, contains the following sub-directories:

Annotations files

  • The annotations folder contains annotations (in GAF and GPAD formats), as well as GPI files. A typical URL for these files is: http://release.geneontology.org/2018-07-02/annotations
  • The file names indicates the file type (GAF; GAPD, GPI) in the extension, for example:
    • mgi.gaf.gz
    • mgi.gpad.gz
    • mgi.gpi.gz

bin

lib

Metadata

  • Information about database cross references used in GO and in annotations, contributing groups, etc

Ontology files

  • GO ontology in OBO, OWL and JSON formats, and in go and go-basic forms
  • extensions -> ?
  • external2go
  • imports
  • reports -> ?
  • subsets

Products

Annotation reports


Types of releases

  • Official monthly releases: versioned and archived so that analyses performed with these data can be reproduced at any point in the future. Note that all files generated as part of the monthly release have a permanent, stable release identifier.
  • Daily snapshot releases: intended for internal use by GOC members. Daily snapshots are not versioned and not archived, therefore not citable. Note that the daily snapshot release is not generated on the day of the official monthly release. Note also that all files generated as part of the snapshot release will NOT have permanent, stable release identifiers.

Consuming and Displaying GO Data

GO Consortium Members

  • To get the most up-to-date data, groups can download data from the 'daily snapshots'; however, for display in public databases and integration in analysis tools, data from Monthly Official Releases should be used.
  • GO annotations should not be changed in any way from their original content, although filtering is allowed.
  • PAINT annotations are available in the 'annotations' files, that also contains all annotations for each given group.
  • PAINT annotations can also be downloaded separately, from the 'products/annotations' directory, where PAINT annotations from each group are current available.

Groups using GO for research and analysis purposes

GO Consortium Dataflow

GO consortium dataflow

Original: https://github.com/geneontology/go-site/blob/master/docs/go-consortium-dataflow.png