Ontology
comment: 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
version info: 0.1
imports: protege

String
type: Class
subclass of: objectClass
subclass of: Restriction
  on property: has string
  has value: true

display
type: Class
comment: takes input object and returns a visual representation of that object - plot, graph, image, etc.
subclass of: bioapplicationService

bioapplicationService
type: Class
comment: a service that performs a task upon biological or objects
subclass of: serviceClass

by translation
type: Class
subclass of: conversion
comment: returns a translation of the input into a different form

conversion
type: Class
version info: TODO: Need to explore this more closely, current subclass structure seems limiting
subclass of: bioapplicationService
comment: takes input object and converts it to another format or representation

find sequence features
type: Class
subclass of: by pattern matching
comment: service searches sequence data for known patterns

deregistration
type: Class
comment: removal of services from central repository
subclass of: registryTransaction

registryTransaction
type: Class
comment: services that send data to and from a registry - that perform a registry transaction of some kind.
subclass of: infrastructureService

analysis
type: Class
comment: a service that performs an bioinformatic analysis upon the input object(s). Inputs are biologically meaningful things.
subclass of: bioapplicationService

database services
type: Class
subclass of: object manipulation
comment: operate on databases to add, delete, update data

object manipulation
type: Class
subclass of: bioapplicationService
comment: manipulation services - take input objects and manipulate them in some way

literature db search
type: Class
subclass of: database search
comment: searches a literature database

database search
type: Class
comment: searches a database using supplied input objects as search criteria, returns a list of hits
subclass of: search

nucleotide db search
type: Class
subclass of: database search
comment: searches nucleotide database

term lookup
type: Class
comment: A dictionary-type service that provides definitions for supplied terms
subclass of: retrieval

retrieval
type: Class
comment: 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.
subclass of: bioapplicationService

align structure
type: Class
subclass of: alignment
comment: alignment using tertiary structure comparison, eg. STAMP

alignment
type: Class
subclass of: analysis
comment: Service that aligns two objects

collection services
type: Class
subclass of: object manipulation
comment: operate on collections of objects

predict property
type: Class
subclass of: analysis
comment: takes input and predicts some property of the input object based on specific algorithms

splitting
type: Class
comment: takes object(s) and breaks apart into subobjects
subclass of: collection services

objectClass
type: Class
comment: root of bioMOBY Object ontology

format parsing
type: Class
comment: 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.
subclass of: bioapplicationService

inserting
type: Class
subclass of: database services
comment: inserts input object into something - database, file

predict tertiary structure
type: Class
comment: prediction of structural features - eg coils, sheets in protein
subclass of: predict structure

resolution
type: Class
subclass of: infrastructureService
comment: provides a resolution service, eg LSID resolution

infrastructureService
type: Class
comment: service that is related to computing infrastructure, does not operate on biological object(s). Eg. performing webservice registration
subclass of: serviceClass

format validation
type: Class
comment: validates the format of the input, eg SQUIZZ tool
subclass of: format parsing

locate feature
type: Class
subclass of: analysis
comment: takes input and finds features based on comparisons to known things, eg. restriction site sequence (as opposed to prediction by algorithm)

calculation
type: Class
comment: service that calculates something: pI of protein sequence, MWt, Hydrophobicity, etc.
subclass of: analysis

predict location
type: Class
subclass of: predict property
comment: 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.

predict sequence feature
type: Class
comment: predicts the existence of various features in the input object through the use of a specific algorithm - eg. gene prediction.
subclass of: predict property

proteinMolecularWeight
type: Class
subclass of: calculation
comment: Calculates a protein's accurate molecular weight

filtering
type: Class
subclass of: collection services
comment: takes group of input objects and filters them by a specified criteria, returns a subset of the group

protein db search
type: Class
subclass of: database search
comment: searches a protein database

has string
type: ObjectProperty
range: Class
comment: has at least one property that is a string
allowed parent: Thing
allowed parent: String

serviceClass
type: Class
comment: Root of the bioMOBY service ontology

find digestion sites
type: Class
subclass of: find sequence features
comment: takes input object and performs digestion, returns collection of subobjects - eg. restriction analysis of DNA, digestion of protein by trypsin, etc.

grouping
type: Class
comment: 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.
subclass of: collection services

by summarization
type: Class
comment: returns a summarized version of the input
subclass of: conversion

proteinIsoelectricPoint
type: Class
subclass of: calculation
comment: calculates a protein's isoelectric point

search
type: Class
comment: Searches a resource using the input object, returns a list of hits matching the search criteria
subclass of: retrieval

nucleotide to amino acid
type: Class
comment: translates a nucleic acid sequence to a protein sequence
subclass of: by translation

by pattern matching
type: Class
comment: searches for the occurance of known pattern(s) - eg. transcription factor binding sites
comment: Not sure if the method should be defined by the ontology at this level
subclass of: locate feature

clustering
type: Class
subclass of: analysis
comment: performs some type of cluster analysis on input data

gene ontology lookup
type: Class
comment: returns term definitions for GO IDs
subclass of: term lookup

find repeats
type: Class
comment: repeat finding in sequence data
subclass of: find sequence features

dictionary lookup
type: Class
subclass of: term lookup
comment: returns the definition of a keyword as defined in a particular dictionary of terms.

dnaMeltingTemperature
type: Class
subclass of: calculation
comment: Calculates the melting point of a given DNA sequence

deleting
type: Class
comment: service deletes data from a database
subclass of: database services

Integer
type: Class
subclass of: objectClass
subclass of: Restriction
  has value: true
  on property: isInteger

registration
type: Class
comment: Allows registration of objects (and/or services) in specified repositories.
subclass of: registryTransaction

merging
type: Class
subclass of: collection services
comment: takes multiple inputs and merges them into a single output

Float
type: Class
subclass of: objectClass
subclass of: Restriction
  on property: isFloat
  has value: true

predictHydropathy
type: Class
comment: Predicts the hydrophilic/hydrophobic proile of a sequence
subclass of: predict structure

pise_tool
type: find sequence features
comment: search prosite patterns in a sequence