The aim of this exercise is to retrieve homologous structures: i) with a developmental origin that changed during evolution, i.e., homologous structures that do not develop from the same organ in different species; ii) with a partonomy relation that varies between species.

Outline

• You will use the annotations provided by Bgee to retrieve anatomical entities that are homologous, see https://github.com/BgeeDB/anatomical-similarity-annotations/wiki/Similarity-annotations
• You will use the Uberon composite-metazoan ontology in OWL to retrieve relations between anatomical entities, see http://uberon.github.io/downloads.html#multiont
• You will use the bgee-pipeline library, owltools and OWLAPI to perform this task (all included in the provided fat jar).
• Java 7 or 8 as you want (but you need to compile in Java 8, as the Bgee pipeline is written in Java 8).

Instructions

• using the bgee-pipeline library, extract the similarity annotations from the file https://raw.githubusercontent.com/BgeeDB/anatomical-similarity-annotations/master/release/ancestral_taxa_homology_annotations.tsv using the method org.bgee.pipeline.annotations.SimilarityAnnotationUtils.extractAncestralTaxaAnnotations(String)

• from the ontology composite-metazoan.owl, and using owltools 0.3-SNAPSHOT and OWLAPI 4.2.5:

  • extract the relations with the object property "develops_from" (see http://purl.obolibrary.org/obo/RO_0002202), or any of its sub-properties, outgoing from anatomical entities present in the similarity annotation file
  • similarly, extract the relations with the object property "part_of" (see http://purl.obolibrary.org/obo/BFO_0000050), or any of its sub-properties

(see in owltools the methods owltools.graph.OWLGraphWrapperExtended.getOWLClassByIdentifier(String), owltools.graph.OWLGraphWrapperEdgesExtended.getOutgoingEdgesWithGCI(OWLObject), owltools.graph.OWLGraphEdge.getTarget(), owltools.graph.OWLGraphEdge.getSingleQuantifiedProperty(), and owltools.graph.OWLGraphEdge.getGCIFiller(); see OWLAPI documentation for related classes)

• Identify homologous structures having ancestors through "develops_from" object properties (or any of its subproperties) that vary between species, if any.

• Identify homologous structures having ancestors through "part_of" object properties (or any of its subproperties) that vary between species, if any.

• Provide the results on a fork of this project on github:

  • create a new folder src/ to provide your source code, organized as you see fit.
  • provide the results in a text format of your choice, allowing an easy retrieval of the relevant information. Highlight the most significant results, if any, in a 1/2 text page. Create a new folder results/ to store these files.