Oort Use Case Cell Cycle

Oort Use Case: the Cell Cycle

Introduction

Goal: create a mouse cell cycle ontology making use of bridging axioms that connect ontologies, compare results with CCO (Antezana et al)

Cell cycle phenotypes

For this use case we are primarily interested in mouse - the mouse phenotype ontology (mp.owl) includes a small number of cell cycle terms:

    is_a MP:0003077 ! abnormal cell cycle *** 
     is_a MP:0004045 ! abnormal cell cycle checkpoint function
      is_a MP:0009762 ! abnormal mitotic spindle assembly checkpoint
     is_a MP:0004046 ! abnormal mitosis
      is_a MP:0003701 ! elevated level of mitotic sister chromatid exchange
      is_a MP:0004759 ! decreased mitotic index
      is_a MP:0004760 ! increased mitotic index
      is_a MP:0009567 ! mitotic nondisjuction
      is_a MP:0009760 ! abnormal mitotic spindle morphology
      is_a MP:0009762 ! abnormal mitotic spindle assembly checkpoint

We may also want to use the two yeast phenotype ontologies (FYPO, APO) as well as OMP.

Biological processes and cell components

        is_a GO:0007067 ! mitosis *** 
         po GO:0000070 ! mitotic sister chromatid segregation
         po GO:0000088 ! mitotic prophase
         po GO:0000089 ! mitotic metaphase
         po GO:0000090 ! mitotic anaphase
         po GO:0000093 ! mitotic telophase
         po GO:0000236 ! mitotic prometaphase
...

Connecting GO to MP

The phenotypes have equivalence axioms connecting them to GO, mouse anatomy, chebi, etc. For now we are primarily interested in go.

• mp/equivalence-axioms.owl

Connecting BP to CC

Some of these axioms may only be in the GO Ontology extensions

E.g.

[[Term]]
id: GO:0051255 ! spindle midzone assembly
intersection_of: GO:0022607 ! cellular component assembly
intersection_of: results_in_assembly_of GO:0051233 ! spindle midzone

We want to follow these links - e.g. for every process that is a cell cycle process, include all components involved, and their closure

This is currently in x-bp-internal.owl

Main input ontologies

So the main put ontologies would be:

• http://purl.obolibrary.org/obo/go.owl
• http://purl.obolibrary.org/obo/mp.owl
• http://purl.obolibrary.org/obo/mp/equivalence-axioms.owl
• http://purl.obolibrary.org/obo/go/extensions/x-bp-internal.owl

Genomic element ontologies and annotation ontologies

We will include both GO and MP annotations, translated to OBO/OWL as well as representation of these genes and associated information (families etc)

Most of the translations of genes will be made available here:

• http://purl.obolibrary.org/obo/ensembl/

(URL may change - ensembl reflects the fact that it came from biomart)

GAFs can be translated to OWL using OWLTools. We will use

• MGI GAF
• Others?

Pathway Data

We can bring in pathway data from Reactome etc. BioPAX3 has to be converted into something more obolibrary-compliant. CJM has code for this, will fill in details later.

Questions

We will take the subset of genes that are related to cell cycle processes. The question is, do we then follow all annotations for those genes (ending up with quite a big chunk of MP and GO) or just those annotations that are to cell cycle related terms