You will be presented with the full text of a biomedical research paper. Please write an abstract for this paper. Your response should include the abstract and no additional text.

Paper text:
ontologies provide domain knowledge to drive data annotation , data integration , information retrieval , natural language processing and decision support . as the number of large data sets are growing , providing a framework for data analysis and data integration using ontologies continues to be of critical importance ( 1 ) .
however , until recently , there has been a lack of common services for accessing this rich content from software applications .
there has also been a lack of services to facilitate ontology development by reusing existing ontology content .
bioportal is a web portal that provides access to a library of biomedical ontologies and terminologies developed in web ontology language ( owl ) , resource description framework ( rdf)(s ) , open biological and biomedical ontologies ( obo ) format , protg frames and rich release format ( http://bioportal.bioontology.org ) .
bioportal has a service - oriented architecture ; the ncbo web services provide the functionality found in bioportal and these web services can be incorporated into other software applications to access and use ontology content .
bioportal groups ontologies by domain to ease finding relevant ontologies and allows users to browse , search and visualize the content of ontologies .
registered users are able to add mappings between terms , to add comments on individual terms within the ontology and to provide reviews of ontologies .
this user - generated content provides critical evaluation and feedback mechanism for ontology developers . the specific focus on enabling community feedback to bioportal
in 2008 , bioportal contained 72 ontologies ( 300  000 total classes ) and has grown significantly over the last 3 years to contain 260 ontologies ( 4.8 million total classes ) .
ontologies from a number of different groups are published in bioportal , including cabig ( https://cabig.nci.nih.gov/ ) , the recipients of clinical and translational science awards ( http://www.ctsaweb.org/ ) , the consultative group on international agricultural research ( http://www.cgiar.org/ ) , the obo library ( http://obofoundry.org/ ) , the proteomics standards initiative ( http://www.psidev.info/ ) , the unified medical language system ( http://www.nlm.nih.gov/research/umls/ ) and the world health organization ( who ) family of international classifications ( http://www.who.int/classifications/en/ ) .
in addition to the increase in ontology content within bioportal , non - biomedical organizations have also installed their own instances of bioportal software .
these organizations include dataone ( http://www.dataone.org/ ) , the marine metadata interoperability project ( http://mmisw.org/orr/ ) and other groups that require official use only levels of privacy for their ontology content and access to the web services ( e.g. annotating hippa regulated data ) or need a repository for ontologies that cover domains not relevant to biomedicine .
when we initially released bioportal , the system included restful web services to get ontology metadata , to get individual ontology terms , to download ontologies and to search within ontologies . since then , we have increased the number of web services to provide expanded functionality and to include web services to create and get ontology views , to get all terms from an ontology , to get instances , to post and get ontology mappings , to post and get comments and to get ontologies and individual ontology terms in rdf .
bioportal is designed to store multiple versions of the same ontology , which enables a historical overview of the ontology as it evolves .
each ontology has a global ( virtual ) ontology identifier and each new version of the ontology has an ontology version identifier .
many of the web services can be called with either the virtual ontology identifier or the ontology version identifier .
ontology subsets are also referred to as slims by the go consortium and value sets when used for structured data entry .
for example , views can serve as value sets to populate a web form select menu or as portions of ontologies to re - use in developing a new ontology .
view web services include functionality to get a list of all ontologies that have views and to create a view using the  view extraction web service .
the view extraction web service is designed to extract branches of ontologies given a term to serve as the root node in the ontology view .
this web service is very popular for generating views of content specific portions of large ontologies such as the ncbi taxonomy , international classification of external causes of injuries ( http://www.who.int/classifications/icd/adaptations/iceci/en/index.html ) and the systematized nomenclature of medicine - clinical terms ( snomed - ct , http://www.ihtsdo.org/snomed-ct ) .
get all terms web service returns the term details for all terms within an ontology .
this web service can be called using a specific ontology version identifier or with the virtual ontology identifier , therefore providing a common web service signature that always returns data from the latest version of the ontology . due to the large size of some ontologies , this
pages of data to minimize the load on both client and server in dealing with extremely large xml files .
the web service is particularly valuable for use of ontology data in other knowledge base systems that require a custom ontology format , such as the ontology management cell from the i2b2 clinical research data management hive ( https://www.i2b2.org/software/index.html ) .
get term web service is now expanded to access instances from owl ontologies . the web service returns 
pages of results containing all instances for a class . based on the design of the ontology , it is useful to access the instances since these may be the terms to use for data annotation .
for example , in the mged ontology the values to specify a requested minimum information about a microarray experiment ( miame ) checklist item are located as instances in the ontology .
the mapping data includes mappings provided by the ontology content providers , for example , mappings based on common concept unique identifiers ( cui ) in umls , mappings specified in obo ontologies through the obo xref property , mappings submitted directly to bioportal by users and mappings generated automatically by algorithms such as loom ( 3 ) .
the mapping web services are parameterized to allow a high degree of flexibility to access the data .
for example , the service can return mappings between individual terms , all mappings for a given term , or all mappings for a given ontology .
the  notes web services provide the ability for registered users to add comments directly to an ontology term or to the ontology .
there are different types of notes that provide varying levels of structure for the note .
comment simply provides a text box to add unstructured comments . however , the  new term proposal note type provides fields to include the preferred name , synonyms , definition and reason for proposing the new term ( figure 1 ) .
each note type has a specific xml response from the notes web service , easily allowing software applications to post or consume the content of the notes web service .
for example , via the service - oriented architecture of bioportal , the notes functionality is being incorporated into the ontology editing software webprotg ( http://protegewiki.stanford.edu/wiki/webprotege ) and could also be incorporated into obo - edit ( http://oboedit.org/ ) .
an email alert system is incorporated into the notes feature , therefore the ontology author and other users interested in comments for a given ontology can be notified via email of new comments .
the ontology author can then engage with the user to address the concern using the notes feature and archive the note once resolved . 

rdf web services are designed to return rdf snippets for individual terms and the content of an entire ontology in rdf .
the goal of the rdf web services is to provide the essential information about a term in rdf .
the rdf term web service returns the term i d , preferred name , synonyms , definitions and super - classes together with selected locally defined annotation properties for the ontology .
the uri for each term is either the original uri present in the ontology file or the uri specified by the respective authority .
if the ontology developers do not provide uris for the terms , bioportal generates these using the purl.bioontology.org server . by generating rdf for the ontologies , the entire content of bioportal ontologies
in addition to the rdf web services , the bioportal prototype sparql endpoint provides access to bioportal ontology content in rdf and is available at : http://sparql.bioontology.org .
tags textual data with ontology terms from bioportal ( 4 ) ; the ncbo resource index web services , which provide access to an ontology - based index of publically available biomedical data ( 5 ) and the ncbo ontology recommender web service ( 6 ) , which given a set of keywords or textual data as input generates a ranked score of which ontology best  covers the data .
we have also wrapped the ncbo web services as widgets for easy embedding of this functionality into web sites .
form autocomplete widget provides variations to fill - in the form menu with the full term uri , term identifier , or the term name ( figure 2 ) .
the  jump to widget also provides the term autocomplete function , but allows users to 
jump directly into bioportal to learn more about the term ( e.g. term details , position in hierarchy , database records annotated with the term ) .
rss feed provides updates on new versions and comments posted to the ontology and can be added to web sites to notify community members of these updates .
graph and  tree widgets provide a way to display an ontology structure on your own web site .
the widgets are available for each ontology in bioportal and the widget code is accessible from the widgets tab . 

widgets are available for all ontologies in bioportal . to view a demo of the widget and get the code to use in your web site , click on the  ontology widgets tab .
widgets are available for all ontologies in bioportal . to view a demo of the widget and get the code to use in your web site , click on the  ontology widgets tab .
bioportal is a web portal that provides access to a library of biomedical ontologies and terminologies via the ncbo web services .
while the overall architecture is domain independent , the ncbo instance is focused on publishing ontology content relevant for biomedicine .
the ontology content in bioportal continues to grow and the usage of the site continues to increase . over the last 2 years
, the number of ontology terms in bioportal has grown by more than an order of magnitude and the number of ontologies increased 4-fold . the usage data for 2010 shows that almost 36  000 unique visitors accessed 35 million pages via the bioportal web services , processing 100  gb of data .
the ease of use of the ncbo web services and widgets provide a convenient mechanism to incorporate ontology content into software applications .
a number of data - annotation applications use ncbo web services , including isacreator ( 7 ) for annotation of high - throughput experimental data , openmdr ( 8) a cabig tool for annotation of data elements relevant to cancer related studies , the ecg gadget ( http://wiki.cvrgrid.org/index.php/ecggadget ) for annotation of electrocardiographs and bioscholar ( https://wiki.birncommunity.org/display/newbirncc/bioscholar ) a tool from birn to construct a knowledge repository derived from pdf files .
the widgets have also been added to a number of web sites to enhance data annotation .
these web sites include redfly , a database of drosophila transcriptional cis - regulatory elements ( 9 ) , the radlex tree browser that provides a radiologist - friendly view of the radlex terminology ( 10,11 ) and the model organism databases such as oryzabase ( 12 ) .
the ncbo web services are facilitating ontology - based search of content in cabig resources and odissea from elsevier that integrates journal publications in sciverse hub with publically available databases via an ontology - based index .
table 1.software applications semantically enabled by ncbo web services and widgetssoftwarencbo technologyurlalexwhttps://alex.med.nyu.edu / portal / atag generatorwhttp://hcls.deri.org / atag / generator / biolitohttp://biolit.ucsd.edu / doc / bioportal reference pluginohttp://protegewiki.stanford.edu / wiki / bioportal_reference_pluginbioportal import pluginohttp://protegewiki.stanford.edu / wiki / bioportal_import_pluginbioscholarohttps://wiki.birncommunity.org / display / newbirncc / bioscholarcgmdrohttp://goo.gl / dvsgmcisbic data managementohttp://www3.imperial.ac.uk / cisbic / corefacilities / datamanagementelemapohttps://victr.vanderbilt.edu
/ elemap / genewikiahttp://en.wikipedia.org / wiki / portal : gene_wikiicatohttp://sites.google.com / site / icd11revision / home / icatisacreatoro , ahttp://isatab.sourceforge.net / isacreator.htmljinxohttp://ncmir.ucsd.edu / downloads / jinx.shtmknowledge eggwhttp://www.kunnskapsegget.no / microsoft word addin for ontology recognitionohttp://ucsdbiolit.codeplex.com / nemo toolkitohttp://nemo.nic.uoregon.edu / wiki / nemo_erp_analysis_toolkitnutritional phenotype databasewhttp://www.dbnp.org / odieahttp://www.bioontology.org / odie - projectodisseao , a , rihttp://www.hub.sciverse.com / ontocatohttp://www.ontocat.org / ontological discovery environmentahttp://ontologicaldiscovery.org / openmdrohttp://citih.osumc.edu / projects / project&r=1032oryzabasewhttp://www.shigen.nig.ac.jp / rice / oryzabase / top
/ top.jspradlex tree browsero , whttp://www.radlex.org / radspeechwhttp://digitaleveredelung.dfki.de / medico - playground / term2.htmlredflywhttp://redfly.ccr.buffalo.edu / rightfieldohttp://www.sysmo - db.org / rightfields3dbohttps://sites.google.com / a / s3db.org / s3db / seekohttp://www.sysmo - db.org / seeksemantic medical image annotationohttp://kithira.biosim.ntua.gr / semiasentient knowledge explorerohttp://www.io - informatics.com / simtkwhttps://simtk.org / home / simtkstrideahttps://clinicalinformatics.stanford.edu / research / stride.htmltriadohttp://triadcommunity.org / tripodahttp://tripod.nih.gov / zoomaohttp://zooma.sourceforge.net / a : annotator web service , o : ontology web services , ri : resource index web service , w : widgets .
software applications semantically enabled by ncbo web services and widgets a : annotator web service , o : ontology web services , ri : resource index web service , w : widgets .
the user group ( https://mailman.stanford.edu/mailman/listinfo/bioportal-user-group ) provides a mechanism to learn more about upcoming features and provide feedback .
national center for biomedical ontology , under roadmap - initiative from the national institutes of health [ grant u54 hg004028 ] .
funding for open access charge : national institutes of health [ grant u54 hg004028 ] .
the national center for biomedical ontology ( ncbo ) is one of the national centers for biomedical computing funded under the nih roadmap initiative . 
 contributing to the national computing infrastructure , ncbo has developed bioportal , a web portal that provides access to a library of biomedical ontologies and terminologies ( http://bioportal.bioontology.org ) via the ncbo web services . 
 bioportal enables community participation in the evaluation and evolution of ontology content by providing features to add mappings between terms , to add comments linked to specific ontology terms and to provide ontology reviews . 
 the ncbo web services ( http://www.bioontology.org/wiki/index.php/ncbo_rest_services ) enable this functionality and provide a uniform mechanism to access ontologies from a variety of knowledge representation formats , such as web ontology language ( owl ) and open biological and biomedical ontologies ( obo ) format . 
 the web services provide multi - layered access to the ontology content , from getting all terms in an ontology to retrieving metadata about a term . 
 users can easily incorporate the ncbo web services into software applications to generate semantically aware applications and to facilitate structured data collection .