hubin-keio
commented
3 years ago Thanks so much, @cmungall . This is really helpful. Yes, col 9 is the annotation column. I have looked into the Python source code that is generated from the schema file and created a separate repository (microbiomedata/pynmdc) so that people can try out the code easily. You, @wdduncan @scanon have been added to this repo, among a few others.
What I need help with is how to:
- Translate 'CDS' to 'SO:0000316,' which is a ControlledTermValue?
- Transliate other features in annotation to ControlledTermValue?
- Define "encodes" in "GeneProduct"
Thanks!
cmungall
dehays
deepakunni3
The schema has inline docs detailing the mapping but we should provide a higher level guide. I will sketch out in this ticket and then this can be turned into docs on the site. I'm doing quickly so if anything is confusing, it's likely I made a mistake. I will also give examples in yaml but the json cognate should be obvious
Example
This GFF line represents the output of structural annotation (the prediction of a CDS on sequence Ga0185794_41). This is given a protein ID (skolemized from reference + coordinates).
Ga0185794_41_48_1037. Col9 represents the outputs of functional annotation. @scanon @hubin-keio do I have this right?The core feature would be represented as an instance of https://microbiomedata.github.io/nmdc-metadata/docs/GenomeFeature
so our initial object would look like:
Note all IDs are prefixed to conform to the NMDC identifiers standards doc
Note the 'encodes' field, to link to a GeneProduct (this will always be a Protein for the current pipeline, but in future we may have ncRNA annotations)
https://microbiomedata.github.io/nmdc-metadata/docs/GeneProduct
Currently the GeneProduct field is fairly bare, but in future additional fields could be added - e.g. AA seq. The GeneProduct is what functional annotations are attached to
https://microbiomedata.github.io/nmdc-metadata/docs/FunctionalAnnotation
Each ';` separated section in col9 of the GFF would correspond to a separate annotation. The annotation links the gene product to the controlled term
Minimally this looks like:
For people familiar with the GO annotation system, each entry here represents a line in GAF or GPAD format files.
There would be one entry for each annotation. Above I am only showing the KO annotation
Note the string KO:K12960 is a key to a controlled term object. An example would be:
This is a minimal representation of the KEGG KO object. It can be linked to other controlled term objects. For example, it can include mappings to other systems (EC), parent/child hierarchies, links to pathways, etc, and these can all be traced to compounds chemical entities. However, we will only support simple KO search for GSP, so I will not detail that here. Please refer to #176 for using pathway knowledge to implement more advanced search.
Annotations to other systems (e.g. Pfam) are handled analogously. Please see the
id_prefixesfield in the schema to see the canonical ID prefix for each system.TODO: document how the feature connects to the metaG/T output
to be discussed