October 2018: This documentation is currently a work in progress.
The information below is intended for GOC members who are providers of annotations. It describes how GOC processes annotations, which can be viewed at locations like AmiGO, downloaded from our sites, and queried via the SPARQL endpoint.
Annotations integrated in the GOC pipeline
- Primary annotations by GOC contributing groups: datasets metadata file.
- PAINT annotations: PAINT datasets metadata file
These annotations are ingested daily.
- Groups wishing to contribute their annotations to GO should have their group added into the GO groups metadata:
- 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.
- Currently all data is ingested from as GAF format.
UniProt-all file is processed differently
Annotation QC checks
- As files are read some lines can be modified or filtered as described in GO Rules Documentation
- A number of checks are ran to ensure the integrity of the data (either at the parsing step or later in the pipeline). 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 identifier).
- report: Violations of the rule are reported but no action is taken by the script.
- Annotation lines that failed a check are reported in Snapshot Annotation Reports.
- Each contributing group currently has a consolidated report rendered as HTML for easier viewing (group-report.html, for example for dictyBase: http://snapshot.geneontology.org/reports/dictybase-report.html)
Annotation merging and file generation
- 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 (predictions) for providing feedback to GOC contributing groups like MODs and UniProt). Once the upstream files have been loaded, checked, and merged, GAFs, GPADs, GPIs, TTLs, reports, and prediction files are produced.
- The exception is annotations produced in Noctua: The GPAD/GPI files produced for the GO-CAM annotations are in Jenkins: http://build.berkeleybop.org/job/export-lego-to-gpad-sparql/lastSuccessfulBuild/artifact/legacy/
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.
Data publishing and access
Data produced by each release can be accessed at the URLs below:
- Current official monthly release: http://current.geneontology.org
- Monthly releases to date: http://release.geneontology.org
- Daily snapshot release: http://snapshot.geneontology.org
- The release content may be accessed from the specific URLs listed above.
- Each page of content is generally organized as:
- Parent (a link to the parent directory)
- Directories (a list of all directories or subdirectories within each specific location)
- Files (a list of all files within each specific location)
- The main list of directories, with information about the content found in each, follows below.
- The annotations directory contains solely annotation files organized alphabetically by contributing group.
- The annotation files available here are those files produced *after* the QC/QA rules have been applied.
- Each group has three files, compressed using the gzip utility:
- Note that the GPI file here corresponds to the GPAD annotation file, not the original GPI file produced by the contributing group.
- An example of annotation files found in the annotation directory:
mgi.gaf.gz mgi.gpad.gz mgi.gpi.gz
- The bin directory contains the binary files used by the GO pipeline to build the release.
- The lib directory contains the libraries used by the GO pipeline to build the release.
- The metadata directory contains relevant metadata used by the pipeline. Examples include:
- datasets.yaml (information about the groups that contribute annotations and where the associated files can be retrieved for the pipeline)
- the list of valid GO_REFs
- the list of GO rules
- The ontology directory contains directories with ontology-related information as well as several different formats of the ontology.
- Much of the content of this directory mirrors what is contained in https://github.com/geneontology/go-ontology/tree/master/src/ontology
- Directories that contain ontology-related information are:
- imports (terms imported from external ontologies used in GO equivalence axioms)
- subsets (the yaml files for metadata on each GO subset)
- Ontology files are:
- TODO: There are also annotation files under the products directory. What are the intended use cases for each of these files?
- wb-prediction.gaf: annotation predictions (from annotation extensions and from Function-Process links) To Be Confirmed
- wb-src.gaf.gz: original source file
- wb_noiea.gaf.gz: original source file parsed and filtered, plus IEA filtered out (no PAINT annotations)
- wb_valid.gaf.gz: original source file parsed and filtered (prior to merging with other files, for eg PAINT)
- species-specific PAINT files
Consuming and Displaying GO Data
GO Consortium Members
- To get the most up-to-date data, groups can download data from the 'daily snapshots', and present that data on their web pages. However, for distributing annotation files, data from an Official Monthly Release must be used. Ideally each MOD should direct their users to their group GAF in the /current/annotations directory: http://current.geneontology.org/annotations.
- 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
- For citation purposes, groups should use the ontology and annotations from the official monthly release and cite the version (date) of the files used.
GO Consortium Dataflow
Last reviewed: August 28, 2018