Frequently Asked Questions
1. What is SAHSAI?
SAHSAI is a web server that automatically extract annotations and intermediate layers of bio-ontologies.
2. Who are primary users of SAHSAI?
Bio-ontology developers, and bioinformaticians who are using bio-ontologies for different applications.
3. What is URI?
A Uniform Resource Identifier (URI) is defined in [RFC3986] as a sequence of characters chosen from a limited subset of the repertoire of US-ASCII [ASCII] characters. URIs refer to resources.
4. Where are the source ontologies used in SAHSAI stored?
SAHSAI uses source ontologies stored in RDF format in He Group SPARQL endpoint in University of Michigan Medical School. The contents of source ontologies are stored in RDF triples and available for SPARQL query. Theoretically, SAHSAI is able to fetch any ontology in a SPARQL queriable RDF server through internet.
5. How can we use SAHSAI to get a single class from source ontology without including a hierarchy of superclasses?
To get a single class using SAHSAI, you can specify the top level source term URI the same as the low level source term URI. Or , you don't need to specify any top level source term URI. By default, SAHSAI fetches a single class unless a top level superclass is specified.
6. Can we use SAHSAI for ontologies developed using OBO format?
SAHSAI is developed based on OWL format. Currently there are many converters that can convert OBO format to OWL format or vice versa. With the help of some converter, it is possible to use SAHSAI for development of a new ontology based on OBO format.
7. How can I use SAHSAI to add new terms and update annotations?
It is recommended that you run SAHSAI again when you like to update your annotations. You may consider to keep one master SAHSAI input file. Whenever you like to add new terms from external ontologies, you can update the SAHSAI input file by adding new term URIs and other related information, and then rerun SAHSAI using our file upload option.
8. Who has used SAHSAI for ontology development? Any successful stories?
SAHSAI has been routinely used for development of the Vaccine Ontology (VO), the Brucellosis Ontology (BO), and the Cell Line Ontology (CLO). We have also tested SAHSAI successfully for importing external ontology terms for development of the Ontology for Biomedical Investigations (OBI). SAHSAI is also being used by many other ontology developers.
9. Why are Basic Formal Ontology (BFO) and Relation Ontology (RO) are better to be imported as a whole?
BFO is the upper level ontology which have been adopted by many domain ontologies developed for scientific research, including those in the OBO Foundry. Similarly, RO is an ontology of core relations used by OBO Foundry ontologies and many other ontologies. Both BFO and RO have relatively small sizes but are essential for ontology development. If you use BFO and RO, you would like to import them as a whole. However, we have also included BFO and RO as source ontologies for SAHSAI importing in case you only want partial importing.
10. How are the input and output files provided by the users stored on SAHSAI servers?
The input and output files are not stored permanently on the SAHSAI servers. They will be stored for up to 24 hours with a unique file name which consists of 8 random characters. These files will be automatically destroyed at 3:00 am EST (New York time) by an internal script. The temporary storage is for users to come back to the input and result files, and it also provides a way for our SAHSAI developers to debug any possible errors. For those users who do have concerns on privacy and security, the users can select to destroy the input and output files immediately in the end of the SAHSAI execution.
11. Can I add more than one term in the SAHSAI input at one time?
Yes. You can add multiple terms in the SAHSAI input file or in the SAHSAI input web form.
12. In SAHSAI input, if I have many low level source ontology terms and many top level source ontology term URIs, how can SAHSAI knows which top level source term URLs are for each low level terms?
SAHSAI can automatically check the hierarchical structure and determine which top level source ontology term URIs can be used for which low level source ontology terms.
13. Is it possible to enter a favorite source ontology and SPARQL end point and then select a different ontology via the drop-down menu?
We do not allow the option of using a favorite source ontology and SPARQL endpoint and at the same time using a different ontology via the drop-down menu. SAHSAI prevents a user from providing two ontology sources. Specifically, when a favorite source ontology and SPARQL endpoint are provided, the drop-down menu does not show any specific ontology. If a different ontology is selected from the drop-down menu, any text in the favorite source ontology input box will automatically be cleared.
14. Is it possible to access SAHSAI programmatically?
Yes. To access SAHSAI without using the SAHSAI web page, try this: curl -s -F file=@/tmp/input.txt -o /tmp/output.owl http://ontofox.hegroup.org/service.php
15. What's the new annotation setting "owl:equivalentClass"?
The annotation setting "owl:equivalentClass" was added on June 9, 2011 to allow the automatic extraction of equivalent class of a specific ontology term(s). Before this setting was separately added, this function of extracting equivalent classes was implemented by default. However, it may generate some confusions, esp. for those who don't know or don't like it. By having it as an individual annotation settign in SAHSAI, we provide users more flexibility.
16. In which cases can the setting "includeAllAxiomsRecursively" be useful?
As described above and in Tutorial, the setting can recursively retrieve all axioms associated with user-specified signature terms. It will in most cases retrieve all results than the setting "includeAllAxioms". Why this feature is useful? It is because often we like to have a more complete view and all terms and annotations directly and indirectly associated with the original signature terms. For example, we may like to have a Functional Genomics Data Society (FGED) view of OBI and use it for the FGED community. In this case, it is better to have a thorough retrieval of all axioms associated with a list of terms specified by FGED. This will allow the implementation of systematic automated reasoning.
17. Do SAHSAI-View and SAHSAI use the OWLAPI modularization code?
No. Neither SAHSAI-View nor the general SAHSAI method uses the OWL API modularization code. Our programs are developed based on SPARQL and PHP coding.
18. What is an ontology axiom?
In the ontology community, axioms are used to associate class and property identifiers (IDs) with either partial or complete specifications of their characteristics, and to give other logical information about classes and properties. These used to be called definitions. However, they are not all definitions in the common sense of the term. Therefore, a more-neutral name "axiom" has been chosen. Reference: http://www.w3.org/TR/2002/WD-owl-absyn-20020729/#5.
19. How to keep updating SAHSAI output results?
The SAHSAI process can be executed at different times to import updated information of external ontology terms. By storing and updating the original SAHSAI input text file, users can subsequently query the SAHSAI server on a regular basis and get up to date information with little effort.
See more information in Tutorial.
