Tutorial

Here we provide a tutorial of how OntoFox can be applied for your research and ontology development:

Many more details about OntoFox and how to use it can be found from our OntoFox manuscript: PubMed ID: 20569493

Table of Contents

1. Source Ontologies and their namespaces
2. OntoFox execution using web input forms
3. OntoFox data input format
4. Four "directives" used in OntoFox
5. Four settings used in OntoFox
6. OntoFox hands on demo
7. OntoFox use case demostrations
8. OntoFox access without using OntoFox web site

1. Source Ontologies and their namespaces:
OntoFox currently includes the following source ontologies for query. OntoFox uses standardized namespaces of source ontologies following OBO Foundry recommendations. These namespaces are also used in ontology servers like Neurocommons.org:

#	Ontology	Base URI	Term URI example
1	CARO	http://purl.org/obo/owl/CARO	http://purl.org/obo/owl/CARO#CARO_0000040
2	CHEBI	http://purl.org/obo/owl/CHEBI	http://purl.org/obo/owl/CHEBI#CHEBI_48999
3	CL	http://purl.org/obo/owl/CL	http://purl.org/obo/owl/CL#CL_0000799
4	DOID	http://purl.org/obo/owl/DOID	http://purl.org/obo/owl/DOID#DOID_12685
5	ENVO	http://purl.org/obo/owl/ENVO	http://purl.org/obo/owl/ENVO#ENVO_00000483
6	FMA	http://purl.org/obo/owl/FMA	http://purl.org/obo/owl/FMA#FMA_9712
7	GO	http://purl.org/obo/owl/GO	http://purl.org/obo/owl/GO#GO_0043152
8	IDO	http://purl.obolibrary.org/obo/	http://purl.obolibrary.org/obo/IDO_0000064
9	MP	http://purl.org/obo/owl/MP	http://purl.org/obo/owl/MP#MP_0000026
10	NCBITaxon	http://purl.org/obo/owl/NCBITaxon	http://purl.org/obo/owl/NCBITaxon#NCBITaxon_263
11	OBI	http://purl.obolibrary.org/obo/	http://purl.obolibrary.org/obo/OBI_0100026
12	PATO	http://purl.org/obo/owl/PATO	http://purl.org/obo/owl/PATO#PATO_0001793
13	PRO	http://purl.org/obo/owl/PRO	http://purl.org/obo/owl/PRO#PRO_000001795
14	SO	http://purl.org/obo/owl/SO	http://purl.org/obo/owl/SO#SO_0001288
15	VO	http://purl.obolibrary.org/obo/	http://purl.obolibrary.org/obo/VO_0000001

The compelete ontologies included in OntoFox is listed here.

2. OntoFox execution using web input forms:
Data for each component can be input using the web input form in the OntoFox home page. OntoFox needs the following information as input from users:

(1) Source ontology: The ontology where a list of terms will be retrieved from.

(2) Low level source term URIs: The URIs of low level term from source ontologies.

(3) Top level source term URIs and tTarget direct superclass URIs: The URIs of top level term from source ontologies and their direct superclass URIs from target ontologies. The top level source term URI can be the same as the low level source term URI. In this case, a single source term will be fetched. If no top level source term is specified, by default the top level source term is the same as the low level source term. Since each top level source term has its own superclass in the target ontology, each target direct superclass of a top level source term should be specified. In OntoFecth, we specify the target direct superclass in a new line, following the sign "subClassOf ".

(4) Setting for retrieving intermediate source terms: Three options are available for retrieving intermediate terms: (a) includeNoIntermediates: no intermediate source terms are retrieved. (b) includeComputedIntermediates: Sensible intermediate source terms are retrieved. Sensible intermediates include those intermediate terms that are closest ancestors of more than one low level source terms. (c) includeAllIntermediates: All intermediate source terms are retrieved.

(5) Source annotation URIs: The annotation URIs for the source terms used in the source ontologies. To map or wrap an annotation to a new one, please specify "copyTo" or "mapTo" in the new line following the orignal annotation URL, followed by the new annotation URI.

The OntoFox home page provide many examples. These examples can be used to quickly learn how to use the OntoFox web forms for OntoFox implementation.

Common annotation URIs:

3. OntoFox data input format:
An example of OntoFox data input file is here:

-----------------------

[Source ontology]
#comment here
#List of ontologies: OBI, NCBITaxon, MP, PATO, GO, DOID, IDO, CHEBI, SO, PRO, CL, ENVO, CARO
NCBITaxon
OBI #another comment here

[Low level source term URIs]
http://purl.org/obo/owl/NCBITaxon#NCBITaxon_263 #Francisella tularensis
http://purl.org/obo/owl/NCBITaxon#NCBITaxon_234 #Brucella
http://purl.org/obo/owl/PATO#PATO_0001793 #right side of
http://purl.org/obo/owl/PATO#PATO_0001792 #left side of

[Top level source term URIs and target direct superclass URIs]
http://purl.org/obo/owl/NCBITaxon#NCBITaxon_2 #Bacteria
subClassOf http://purl.obolibrary.org/obo/OBI_0100026 #organism, this term is from target ontology
http://purl.org/obo/owl/PATO#PATO_0001238
subClassOf http://www.ifomis.org/bfo/1.1/snap#Quality #Note: Use designated sign "subClassOf"

[Source term retrieval setting]
includeNoIntermediates #or: includeAllIntermediates, inincludeComputedIntermediates

[Source annotation URIs]
http://www.w3.org/2000/01/rdf-schema#label
copyTo http://purl.obolibrary.org/obo/IAO_0000111
http://www.geneontology.org/formats/oboInOwl#hasDefinition
mapTo http://purl.obolibrary.org/obo/IAO_0000115
http://www.geneontology.org/formats/oboInOwl#hasSynonym

-----------------------

As you can tell, the OntoFox data input format contains the following components:

1. Headings: Each heading contains a text description quoted inside parenthesis "[ ]". Five headings represent the four components of OntoFox execution. Please use the exact same text in all headings.
2. Source ontology list under the first heading. This is required. If using web forms, one or many ontologies can be selected. Currently, the ontologies we have tested and included in OntoFox include: OBI, NCBITaxon, MP, PATO, GO, DOID, IDO, CHEBI, SO, PRO, CL, ENVO, and CARO.
3. Low level source term URIs: At least one source term URI is required.
4. Top level source term URIs and target direct superclass URIs: Since each top level source term has its own direct superclass in the target ontology, URIs of target direct superclasses of individual top level source terms are input together with the top level source term with a new line starting with "subClassOf". To get a single class from source ontology, you do not need to specify any top level source term, or you can specify the top level source term URI as the same as the low level source term URI.
5. Source term retrieval setting: Choose one of three settings for retrieving intermediate source ontology terms:: includeNoIntermediates, includeAllIntermediates, and inincludeComputedIntermediates. See description below.
6. Source annotation URIs: The source term annotation URIs are requested in case only limited annotations are needed. If no annotation URI is assigned, no annotations associated with a specific ontology term will be fetched. To include all possible annotations, you can put "includeAllAxioms"on one line, and all the annotations associated with a specific ontology term will be fetched. To map or wrap an annotation to a new one, please specify "copyTo" or "mapTo" in the new line following the orignal annotation URL, followed by the new annotation URI.
   
7. Comments: The sign "#" as the first letter of a line or as a letter after a space in the middle of a line is an indicator of a comment. All text after this sign within one line is considered comment and will not be used for OntoFox analysis.

4. Four "directives" used in OntoFox:
Four directives are designed as unique OntoFox commands to guide users to provide consistent and readable input data in OntoFox web forms or input text format

1. "fromEndpoint": This directive is generated to indicate a SPARQL endpoint from which a source ontology is retrieved by OntoFox. It is used at the beginning of a line, followed by a web-accessible URL of a particular SPARQL endpoint. The line above this ‘fromEndpoint’ statement is the URI of a source ontology.
2. "subClassOf": This is a directive that is used in defining the target direct superclass (Box 3). This directive should be the first word in a line, followed by a target ontology URI that will be the superclass of the source ontology term listed in the previous line.
3. "copyTo": This is a directive that is used in mapping for ontology term annotation (Box 4). This directive should be the first word in a line, followed by an annotation URI used in target ontology. The use of this directive would lead to addition of an annotation to an imported term which includes an annotation with annotation URI specified in the line before "copyTo". For example, the "copyTo" in the above example will provide an additional annotation http://purl.obolibrary.org/obo/IAO_0000111 (preferred_term) with the same content as the "label" (http://www.w3.org/2000/01/rdf-schema#label).
   
4. "mapTo": This is a directive that is used in wrapping for ontology term annotation (Box 4). This directive should be the first word in a line, followed by an annotation URI used in target ontology. The use of this directive would lead to replacement of an annotation (specified by the annotation URI in the line before) of an imported term with another annotation specified in the URI following "mapTo". For example, the "mapTo" in the above example will replace source ontology annotation term URI "http://www.geneontology.org/formats/oboInOwl#hasDefinition" with target ontology annotation term URI "http://purl.obolibrary.org/obo/IAO_0000115" (IAO definition).

5. Four settings used in OntoFox:
Four OntoFox settings are designed to allow OntoFox server parse needed information. Any of these OntoFox settings stands alone and does not procede or follow any statements:

1. “includeNoIntermediates”: no intermediate source terms are retrieved.
2. “includeComputedIntermediates”: Computed intermediate source terms include those intermediate terms that are closest ancestors of more than one low level source terms. Those intermediate terms that have only one parent term and one child term each are removed. This setting provides an option to get less intermediate ontology terms then that with the setting ‘includeAllIntermediates” and still fulfills many users’ requirement. This option is the default usage for many ontologies (e.g., VO and OBI).
3. “includeAllIntermediates”: All intermediate source terms are retrieved.
4. "includeAllAxioms": By default, if no annotation URI is assigned, no annotations associated with a specific ontology term will be fetched. To include all possible annotations, you can put "includeAllAxioms"on one line, and all the annotations associated with a specific ontology term will be fetched.

8. Remote OntoFox access without using the OntoFox web page:
We understand that there probably is a need to access OntoFox programmatically without coming to OntoFox web page. For this purpose, we have generated a new php script: http://ontofox.hegroup.org/service.php. For example, a user can use the following command line code to get the result: "curl -s -F file=@/tmp/input.txt -o /tmp/output.owl http://ontofox.hegroup.org/service.php". Alternatively, a user can also develop code using Perl, Java or other programming languages. In this case, a user will need use "put" to access this page.