Difference between revisions of "Noctua MOD Imports"

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===== GP ' acts upstream of (or within)' BP =====
 
===== GP ' acts upstream of (or within)' BP =====
** For existing GP 'acts upstream of or within' BP:
+
* For existing GP 'acts upstream of (or within)' BP:
 
*** [GP] <-enabled_by (GO:0003674 molecular_function) causally_upstream_of_or_within -> BP
 
*** [GP] <-enabled_by (GO:0003674 molecular_function) causally_upstream_of_or_within -> BP
 +
***[http://noctua-dev.berkeleybop.org/editor/graph/gomodel:74b7f3b6-9ea0-45b7-8a7a-971a27b6e430 Example: mouse Rela]
  
 
=== References ===
 
=== References ===

Revision as of 07:28, 18 March 2019

Introduction

This page contains documentation for importing a set of MOD annotations into Noctua as GO-CAMs (Gene Ontology Causal Activity Modeling). This initial set of guidelines is based on a set of general import rules that have been further refined by testing the imports with annotations from MGI and WormBase. We expect that each group that imports their annotations may have some unique issues that will need to be dealt with on an individual basis, but these guidelines are nevertheless intended to give all groups a point from which to begin the process.

Import Files

Annotation Sets Imported

  • MODs will import their manual GO annotations, e.g Assigned_by 'MGI'.
    • At this time, annotations made to the same species by external groups will not be imported.
    • MODs may choose to include/exclude annotations made with specific evidence codes, but the overall goal is to get a full set of manual annotations imported as GO-CAMs.

Import File Format

  • The annotation import pipeline uses the GPAD annotation file format.
  • Using GPAD file format allows us to import key information not in the GAF:
      • all gene product-to-term (gp2term) relations
      • annotation metadata in the Annotation_property field
  • The GPAD file used for annotation import may likely be a 'one-off' file that includes metadata stored in other curation tools that would not normally be output in the GPAD file consumed by our users.

Modeling Conventional Annotations as GO-CAMs

One Gene = One GO-CAM

  • Each gene's set of conventional annotations will be imported as one GO-CAM.
  • Annotations with no extensions are modeled very simply, while annotations with extensions are converted to a GO-CAM model that most faithfully represents the information captured in the extension.
    • Note that not all relations used in annotation extensions are used in Noctua and GO-CAMs, so the exact translation of an extension to a GO-CAM is not always possible. However, in these cases, we have tried very hard to capture the information in a clear, consistent way.

Basic Rules

Molecular Function

Cellular Component

Biological Process

  • Biological Process annotations are modeled with respect to Molecular Function, as this is the GO-CAM convention.
    • All Molecular Functions will be to the root node; this is the most conservative approach.
    • Note that these root MF annotations will NOT be exported in the GPAD file.
  • Relations between the root MF and BP will be derived from existing gene product-to-Biological Process relations in the GPAD.
GP 'involved in' BP
  • These will be modeled as root MF 'enabled by' GP is 'part of' a BP.
GP ' acts upstream of (or within)' BP
  • For existing GP 'acts upstream of (or within)' BP:
      • [GP] <-enabled_by (GO:0003674 molecular_function) causally_upstream_of_or_within -> BP
      • Example: mouse Rela

References

  • Will import one reference ID in order of preference:
    • PMID
    • GO_REF
    • doi
    • MOD paper id

With/From Field

  • github ticket on modeling multiple values in the With/From field in OWL, i.e. commas and/or pipes
  • For now, import as strings?
  • Future project may be to develop and use OWL Union and Intersection to represent what is meant by commas and/or pipes in the With/From field

Annotation Extensions

  • Working with Dustin and Paul to devise a set of rules to convert existing annotation extensions to GO-CAM
  • [https://docs.google.com/spreadsheets/d/1AEAj39mxQnBsuccIxWhpjiFKcdCJLw6uIa1eXiAG1Hs Google spreadsheet of annotation extensions for which the meaning and/or conversion needs to be clarified
  • This is currently where the bulk of the curator work is being done
    • For example, has_regulation_target extensions need to be modeled for GO-CAM