BioMOBY service ontology v2, Simon Twigger, 2004. This ontology is intended to be used by MOBY services as a way of classifying the function of that service in a standard fashion. This will enable more precise service discovery by users/applications
takes input object and returns a visual representation of that object - plot, graph, image, etc.
returns a translation of the input into a different form
TODO: Need to explore this more closely, current subclass structure seems limiting
takes input object and converts it to another format or representation
removal of services from central repository
a service that performs an bioinformatic analysis upon the input object(s). Inputs are biologically meaningful things.
operate on databases to add, delete, update data
A dictionary-type service that provides definitions for supplied terms
alignment using tertiary structure comparison, eg. STAMP
takes input and predicts some property of the input object based on specific algorithms
takes object(s) and breaks apart into subobjects
service that takes an input and parses it, analyzing the parts of the input document, returning an organized collection of the parts back to the calling application.
inserts input object into something - database, file
prediction of structural features - eg coils, sheets in protein
provides a resolution service, eg LSID resolution
validates the format of the input, eg SQUIZZ tool
takes input and finds features based on comparisons to known things, eg. restriction site sequence (as opposed to prediction by algorithm)
service that calculates something: pI of protein sequence, MWt, Hydrophobicity, etc.
predicts the physical location of the input object based on some analysis - eg. protein location within the cell based on signal peptide, transmembrane regions, etc.
predicts the existence of various features in the input object through the use of a specific algorithm - eg. gene prediction.
Calculates a protein's accurate molecular weight
services that send data to and from a registry - that perform a registry transaction of some kind.
takes group of input objects and filters them by a specified criteria, returns a subset of the group
service that is related to computing infrastructure, does not operate on biological object(s). Eg. performing webservice registration
a service that performs a task upon biological or objects
takes input object and performs digestion, returns collection of subobjects - eg. restriction analysis of DNA, digestion of protein by trypsin, etc.
takes a list of input objects and groups them accoring to criteria, returns a collection of the grouped objects or the same list with group information included.
returns a summarized version of the input
calculates a protein's isoelectric point
Service thats main function is to take an input and retrieves information related to the input, eg. using a term to retrieve a definition, a genbank accession to get a flat file.
searches a database using supplied input objects as search criteria, returns a list of hits
translates a nucleic acid sequence to a protein sequence
service searches sequence data for known patterns
manipulation services - take input objects and manipulate them in some way
searches for the occurance of known pattern(s) - eg. transcription factor binding sites
Not sure if the method should be defined by the ontology at this level
performs some type of cluster analysis on input data
returns the definition of a keyword as defined in a particular dictionary of terms.
Calculates the melting point of a given DNA sequence
Searches a resource using the input object, returns a list of hits matching the search criteria
Allows registration of objects (and/or services) in specified repositories.
takes multiple inputs and merges them into a single output
Predicts the hydrophilic/hydrophobic proile of a sequence
has at least one property that is a string