I'd like to annotate features of protein structures semantically e.g. "helix Z is kinked", "hydrogen bond between residue Y and ligand X", "structure in closed conformation", "has cleft". Which ontolog(y/ies) should I use/combine?
Couple of links that might help.
Protein Ontology - has several sets of terms that relate to structure - domains, bonds, atoms, chains and so on.
The Protein Feature Ontology: a tool for the unification of protein feature annotations is from Janet Thornton's group, so you'd assume it's worth looking at. I'm not sure how detailed the structural terms are - it seems to be geared more towards domains and functional annotation, just from a first glance.
Probably also worth exploring the PDB - in particular, some of the XML schema that they use could give you some ideas about appropriate terms.
Not a direct answer, but you might find this kind of ontology on bioportal
If the ontology you need does not exist, you might create it with Protege
Just having a quick browse on the OBO Foundry website (disclaimer: I'm a big fan of OBO ontologies):
has several that might be of interest to you:
PRotein Ontology (PRO)
Protein covalent bond
Protein Domains
Protein modification
Hope some of these may be of use to you. Where possible I'd try not to create my own ontology, due to the work involved, YAO syndrome (yet another ontology) and the maintenance required.
HTH
I am not sure if any of the available protein structure based ontology can give semantic structure like "helix Z is kinked" or "structure in closed conformation". This information requires extensive manual annotation of structures and I am not sure if there is any such curated resources from PDB or based on PDB.
As other members suggested here : AFAIK - there is only 3 major Ontology associated with structure. The first two is already mentioned here:
Protein Ontology : see the hierarchy of ontology here. This will be the one close to what you are looking for. But it is limited to primary structural features.
Protein feature Ontology from Thornton's group is not exclusively for structures, it reports features mainly from Sequence Ontology. A more recent version of SO is available here
If you are interested in GO annotation associated with protein structures. You may look in to SCOP2GO, this is a mapping of GO terms to SCOP domains using significant association of terms with SCOP domains. An alternate way to get GO terms associated PDB is to look in PDB2GO association file from GOA.
@Marcin : You may consider the ontology defined in PO if you are planning to design a new ontology. I am not sure if PFO is an active project at the moment and I have a strong feeling that it is now merged in to SO, which is fairly active and maintained.
Part of my thesis work is based on 3D domain swapping in proteins, please let me know if you would like to define some terms related to 3D domain swapping for your structure based ontology.
Marcin : You may consider the ontology terms defined in PO if you are planning to design a new ontology. I am not sure if PFO is an active project at the moment and I have a strong feeling that it is now merged in to SO, which is fairly active and maintained. Part of my thesis work is based on 3D domain swapping in proteins, please let me know if you would like to define some terms related to 3D domain swapping for your structure based ontology. I will be happy to pitch in.
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version 2.3.6
self comment, it's kind of funny that The Open Protein Annotation System (TOPSAN http://topsan.wordpress.com/) uses only yet another ontology for database cross-references.
in case anyone is interested there is also: http://www.semanticoverflow.com/ with all the hairy semantic disussions