View source for Noctua MOD Imports

'''Note: the rules for MOD imports into Noctua are still under revision.  If you have any questions about specific rules, please enter a ticket in https://github.com/geneontology/gocamgen before doing any annotation revision.'''

= 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_properties 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 ===

'''Note: iterations of import rules are being tested on noctua-dev.berkeleybop,org'''

'''Specific tests and the outcomes can be found on this [https://docs.google.com/spreadsheets/d/1XFuD6LOyFKXNk94jIK8zv1TrESfwCJo-RnrXQ3tzmJg/edit#gid=0 Google spreadsheet]'''

==== Molecular Function ====
* [GP] <- enabled_by [MF]
** Example: C. elegans atg-18 - WBGene00018294
* [GP] contributes_to -> [MF]
**Example: C. elegans pptr-1 - WBGene00012348

===== Protein Binding Annotations =====
'''Note: [https://github.com/geneontology/gocamgen/issues/50 new ticket] in to generalize this rule to all annotations to 'binding' or a descendant'''
*Currently, GO-CAM models annotate protein binding differently than conventional annotation.  
*The difference is that the interacting partner(s) is captured as contextual information using the 'has input' relation.
*In conventional annotation, the interacting partner is typically captured using the With/From field, although if the experimental interactor is not from the same species, the biologically relevant interactor may also have been captured using the has_input relation.
*Our decision for how to import protein-binding annotations is as follows:
**Entries in the With/From field will be used to populate 'has input' to 'protein binding' (GO:0005515) or one of its children
***Single entries in the With/From field can simply be converted to a single value 'has input'
***Multiple, comma-separated entries in the With/From field can be converted to multiple 'has input' on a single binding term
***Multiple, pipe-separated entries in the With/From field will need to be split out into separate protein binding instances, each with its own 'has input' value consistent with the above rules for single or multiple, comma-separated values
**Upon export in GPAD, the value(s) in the 'has input' field will be added back to the With/From field
*Evidence will not be combined for annotations to protein binding or its children unless the entry in the With/From field is the same
*Relevant github ticket: https://github.com/geneontology/gocamgen/issues/45

==== Cellular Component ====
* [GP] part_of -> [CC]
**Example: C. elegans epg-6 - WBGene00012641
* [GP] colocalizes_with -> [CC]
**Example: C. elegans mlc-4 - WBGene00003372

==== 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] <- 'enabled by' (GO:0003674 molecular_function) 'part_of'-> BP
**Example: C. elegans ogt-1 - WBGene00003858

===== GP ' acts upstream of (or within)' BP =====
* [GP] <-enabled_by (GO:0003674 molecular_function) causally_upstream_of_or_within -> BP
** Example: mouse Rela - note that this rule is not implemented yet
** Positive effect example: 
** Negative effect example:

=== References ===
*Where multiple, pipe-separate references exist for a single annotation, only one reference ID is imported in order of preference:
**PMID
**GO_REF
**doi
**MOD paper id
*Models when there is multiple evidence to support a given GO annotation:
**If multiple, independent references exist to support a given annotation, do we want to combine them or leave them separate?  What are the implications for later model manipulation?
**Combining evidence on to a single edge wherever possible will simplify the graph display, but may make moving or merging annotations later more complicated.

=== With/From Field ===
*Values in the With/From field will be imported as string literal, i.e. text will be imported "as is" with no further modeling in the OWL representation 
*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
*Relevant github ticket(s):
**[https://github.com/geneontology/gocamgen/issues/21 github ticket] on modeling multiple values in the With/From field in OWL, i.e. commas and/or pipes

=== Annotation Extensions ===
* Rules for importing annotation extensions address cardinality, domain and range constraints, and modeling when an extension relation is not used in Noctua.
*Pipe-separated annotation extensions are treated as separate annotations.
*[https://docs.google.com/spreadsheets/d/1AEAj39mxQnBsuccIxWhpjiFKcdCJLw6uIa1eXiAG1Hs Google spreadsheet of annotation extensions for which the meaning and/or conversion needs to be clarified]

==== Simple Conversions ====
* These simple conversion rules are derived from a set of rules that Paul T. and Dustin put together.
* Some existing annotations violate these rules, so it will be necessary to review those and make sure we're clear on what was meant by the annotation before we relax the rule.

===== Molecular Function =====
*No more than one occurs_in(CC)
*No more than one occurs_in(CL)
*No more than one happens_during(BP)
*No more than one part_of(BP)
*No more than one activated_by(ChEBI)
*No more than one inhibited_by(ChEBI)
*No more than one occurs_in (UBERON)
*No more than one occurs_in (EMAPA)
Multiple values allowed:
*WBbt (contains both cell and anatomy terms)
*has_input/has_direct_input(geneID or ChEBI)
**'''has_direct_input will be converted to has_input upon import'''

===== Cellular Component =====
*No more than one part_of(CC)
*No more than one part_of(CL)
*No more than one part_of(UBERON or EMAPA)
*No more than one exists_during(GO:BP)
*No more than on exists_during(WBls)
Multiple values allowed:
*WBbt (contains both cell and anatomy terms)

===== Biological Process =====
*No more than one occurs_in(CC)
*No more than one occurs_in(CL)
*No more than one part_of(BP)
*No more than one happens_during(BP)
**How many of these are really part_of(BP)?
Multiple entries allowed?:
*occurs_in(UBERON)
*occurs_in(EMAPA)
Multiple values allowed:
*WBbt (contains both cell and anatomy terms)
*has_input/has_direct_input(geneID or ChEBI)

==== Other Conversions ====
===== has regulation target =====
* The rules below are still being tested and may be further refined.
====== regulation of molecular function ======

====== BP descendants (currently re-visiting this rule) ======
*Annotated term is 'regulation of molecular function' (GO:0065009) or BP descendant
*Expressed as [GP-A]<-enabled_by-[root MF]-part_of ->[regulation BP]-regulates -> [MF-Z] enabled_by ->[GP-B]
**Note that MF Z should appear in the logical definition of the term “regulation of MF Z” (or in a triple with the regulates relation, so we can get the GO ID from that).
***For example:
****'regulation of histone deacetylase activity' (GO:1901725) is defined as: 'biological_process' and (regulates some 'histone deacetylase activity')
*The variations on this are all children of the term “regulation of molecular function” (GO:0065009).
*Proposed directional variations are:
***“positive regulation of MF Z” and children which would be expressed with the positively_regulates relation instead.
***“negative regulation of MF Z” and children which would be expressed with the negatively_regulates relation instead.

====== MF descendants ======
*Annotated term is 'molecular function regulator' (GO:0098772) or descendants
*Generally expressed as [GP-A]<-enabled_by-[root MF]-regulates->[MF Z]-enabled_by->[GP-B]
*Molecular function activators:
**[GP-A] <- enabled_by - [root MF] - directly_positively_regulates -> [MF-Z] - enabled_by ->[GP=B]
*Molecular function inhibitors:
**[GP-A] <- enabled_by - [root MF] - directly_negatively_regulates -> [MF-Z] - enabled_by ->[GP=B]
*Example: enzyme activator activity
**molecular_function and ('directly positively regulates' some 'catalytic activity')

====== regulation of gene expression ======
*GP-A [regulation of gene expression Z] has_regulation_target GP-B
*These can be modeled as GP-A<-enabled_by-[root MF]-part_of->[regulation of Z]-has_input->GP-B,-causally upstream of (positive/negative effect)->[root MF]-enabled_by->GP-B
*Will be positively or negatively causally upstream of instead, if in the original term.

====== regulation of protein metabolic process ======
*GP-A [regulation of protein metabolic process Z, not including cases above, or regulation of protein localization] has_regulation_target GP-B
*These are GO:0019538 and the descendants that are not also descendants of terms listed above
*These can be modeled as GP-A<-enabled_by-[root MF]-part_of->[regulation of Z]-has_input->GP-B

====== regulation of protein biosynthetic process ======
*GP-A [regulation of protein biosynthetic process Z] has_regulation_target GP-B
*These can be modeled as GP-A<-enabled_by-[root MF]-part_of->[regulation of Z]-has_input->GP-B,-causally upstream of (positive/negative effect)->[root MF]-enabled_by->GP-B
*Will be positively or negatively causally upstream of instead, if in the original term.

====== regulation of protein catabolic process ======
*GP-A [regulation of protein catabolic process Z] has_regulation_target GP-B
*GO:0042176 and descendants

====== regulation of receptor internalization ======
*GP-A [Regulation of receptor internalization (GO:0002092) Z] has_regulation_target GP-B
*These are GO:0002092 and descendants
*These can be modeled as GP-A<-enabled_by-[root MF]-part_of->[regulation of Z]-has_input->GP-B,-causally upstream of (positive/negative effect)->[root MF]-enabled_by->GP-B
*If term is positive regulation, relation will be causally upstream of, negative effect; if negative reg, relation will be causally upstream of, positive effect

====== regulation of protein localization ======
*GP-A [regulation of protein localization] has_regulation_target GP-B
*GO:0032880 and descendants
*These can be modeled as GP-A<-enabled_by-[root MF]-part_of->[regulation of Z]-has_input->GP-B

=== Multiple Extensions ===
Rules for importing annotations with multiple, comma-separated annotation extensions.

=== Chained Relations ===
*regulates_o_results_in_specification_of
*regulates_o_results_in_movement_of

=== GPAD Output Files ===





[[Category:GO-CAM]]