Editorial process

Contents

1 Design Principles for the NPO
2 Process for Maintenance and Extension
3 Quality Assurance and Quality Control
4 Methods for Enriching the Ontology for Domain Coverage
5 Availability of NPO
6 Release Cycles
7 Community Acceptance

Summary

Here we provide the principles and mechanisms for performing activities involved in the design, creation, distribution and maintenance of the NanoParticle Ontology (NPO).

Design Principles for the NPO

The main design principles used in developing the NPO are listed below. These design precepts are based on BFO and Open Biomedical Ontologies (OBO) Foundry principles (http://www.obofoundry.org/crit.shtml) as well as our review of other OWL-encoded ontologies and controlled vocabularies:

Principle of unbiased representation

Following BFO design principles, any term in the ontology should represent an entity as known in reality and not represent it from the biased view of an individual.

Principle of asserted single “is_a” inheritance

Again following BFO principles, each term should have no more than one parent term in the asserted OWL hierarchy. This principle offers the advantages of making the ontology easily extensible and interoperable with other ontologies that have a formal structure. This single-parent structure also helps to build the ontology in a modular fashion whereby different parts of the ontology can be worked on independently.

Principle of inferred multiple “is_a” inheritance

Multiple parent-child relationships for a term are not present in the asserted hierarchy. However, a term can have more than one parent in the inferred hierarchy that is constructed by invoking an appropriate “OWL reasoner” (e.g., Pellet) on the asserted hierarchy. Rules for inferring these relationships are expressed using OWL description logic and specified as OWL necessary and sufficient or necessary conditions, in the ontology. The OWL reasoner uses the OWL expressions to create the inferred hierarchy.

Sibling disjointedness

Unlike in the BFO, axioms for disjoint sibling classes are not enforced at all levels in the asserted OWL hierarchy. The disjointedness is maintained at the upper level of the ontology formed by the BFO classes. If sibling disjointedness is applied at a level of the asserted OWL hierarchy, then the following principles are considered:

Disjointedness is applied only between primitive sibling classes.
Disjoint axioms are applied to primitive sibling classes only after the hierarchical level containing the classes is exhausted, such that any class added later will not have instances that overlap with the instances of existing sibling classes.

Preferred name and definition

Every OWL class and OWL property (object, datatype) must have a preferred name and a textual definition using the NPO’s OWL annotation properties: “preferred name” and “definition”.

Synonym

If a class or OWL property has multiple names, these names must be provided as synonyms using the NPO’s “synonym” OWL annotation property.

External class reference

Classes borrowed from external sources should be given their external reference ID using the “dBXrefID” annotation property. A term may have multiple dBXrefIDs if it has mappings to more than one terminology.

Code

Every class must have an identification code that starts with the prefix “NPO_” (e.g., NPO_100).

rdf:ID and rdf:Label

Every class specifically defined in the NPO must have an rdf:ID that has a value same as the NPO code The rdf:ID of every class borrowed from an external ontology found in the OBO Foundry list, must be preserved in the NPO. Every class in the NPO must also have its preferred name as its rdf:Label.

Process for Maintenance and Extension

Mechanism for permanent storage

Versions of the NPO are released as OWL files through BioPortal for visualization and download (http://purl.bioontology.org/ontology/npo). The NPO will also be available on the BiomedGT semantic media wiki (SMW) at http://biomedgt.nci.nih.gov/wiki/index.php/NPO for facilitating collaborative development of ontology with the community.

Mechanisms for handling changes

Proposal for minor/major changes (additions, refinements, disambiguation, name changes, etc.) to the NPO will be managed through the BiomedGT SMW where subject matter experts or users of the NPO can review, evaluate and propose changes to the ontology. Through the proposal workflow of BiomedGT, the proposals will be retrieved from the wiki and curated by an ontology developer for incorporation into the NPO through the NCI Protégé Editor. (Documentation of the proposal processes can be found at http://biomedgt.nci.nih.gov/wiki/index.php/Scenarios_Discussion and http://biomedgt.nci.nih.gov/wiki/index.php/Data_Flows .)

The ontology developer will record any changes (and the reasons for these changes) made in the NPO into a spreadsheet file which will be released as “release notes” on the NPO documentation wiki (http://www.nano-ontology.org/).

These changes will be recorded under the following categories:

New OWL classes and properties

New OWL classes
New OWL object properties
New OWL annotation properties

Collective changes to OWL classes and properties
Specific changes to OWL properties from previous version (yyyy-mm-dd)

Specific changes to OWL object properties
Specific changes to OWL annotation properties

Specific changes to OWL classes

Specific changes to class-level annotation

New class-level annotation
Changes to class-level annotation from previous version (yyyy-mm-dd)

Specific changes to class-level assertion

New class-level assertion
Changes to class-level assertion from previous version (yyyy-mm-dd)

Mechanisms for handling term deprecation

Mechanisms are required to indicate which term is deprecated, why it is deprecated, and to indicate if another term replaces the deprecated one. These mechanisms will be borrowed from the NCI Protégé editor workflow (details found in Chapter 9 of NCI Protégé v. 1.2. editor’s guide - https://cabig-kc.nci.nih.gov/Vocab/KC/index.php/NCI_Protégé).

Mechanisms for identifying new terms

Manual mechanism

New terms are identified manually using information about the chemical composition, preparation, physicochemical characterization, in vitro characterization and in vivo characterization of nanomaterials. The main sources for this information are the literature, the caNanoLab database, data submission into NanoTAB, and other ontologies / controlled vocabularies (e.g., ChEBI, NCI Thesaurus, GO, FIX, etc.).

Semi-automated mechanism

Terms from literature such as journal articles can also be obtained using text-mining tools such as Termine (http://nactem.ac.uk/software/termine)

Re-use of terms from other ontologies / controlled vocabularies

After identifying new terms, the ontology developer searches for these terms in other ontologies and controlled vocabularies (CVs). If the terms exist in external ontologies / controlled vocabularies, the developer will re-use these terms and adapt them into the NPO according to the design principles stated in Part A. Sources for searching these terms will be the ontologies and CVs available through the NCBO BioPortal (http://bioportal.bioontology.org/search), the EVS NCI Term Browser (http://nciterms.nci.nih.gov/ncitbrowser/pages/vocabulary.jsf?dictionary=Nanoparticle%20Ontology&version=2011-02-12), and EMBL-EBI database (http://www.ebi.ac.uk/).

Mechanisms for identifying redundancy

Redundant terms are identified manually by searching the NPO after loading the OWL file in the Protégé OWL editor. Redundancy is avoided while adding new terms by first searching for similar terms (e.g., terms with a name that could be synonymous with the preferred name of a new term) in the NPO.

Quality Assurance and Quality Control

Language

The NPO should only be edited in the English language.

Detection and elimination of errors in modeling and/or editing

We will use a reasoner (e.g. Pellet OWL reasoner) to classify the ontology in order to check for any inconsistencies within the class-level assertions. Detection and elimination of errors in the annotation of classes and object properties will be done manually as they are edited.

Review by independent experts who are SMEs or users of the NPO

Independent experts will be able to review and evaluate the NPO through the BiomedGT SMW.

Improvement of the NPO based on feedback by the experts through the BiomedGT SMW

The ontology developer will obtain the proposals submitted by the experts on the BiomedGT SMW based on the BiomedGT proposal workflow and NCI Protégé editor workflow processes.

Methods for Enriching the Ontology for Domain Coverage

The domain coverage will span the knowledge underlying the chemical composition, preparation, physicochemical characterization, in vitro characterization and in vivo characterization of nanomaterials that are developed for cancer therapeutics and diagnostics.

Manual enrichment of the ontology will take place as more terms are identified from the literature, as data annotation is required in both caNanoLab and nano-TAB and through the user feedback and requirements.

Semi-automatic enrichment methods such as the use of text-mining tools and ontology-based information extraction tools (e.g. ODIE tools) will be pursued to facilitate the identification and collection of terms from a literature corpus.

Availability of NPO

The NPO is available in OWL format and can be freely downloaded from the NCBO BioPortal. The NPO can be browsed and visualized through the NCBO BioPortal and the EVS NCI term browser (http://ncit.nci.nih.gov/ncitbrowser/start.jsf). The NPO can be visualized and evaluated by SMEs and NPO users through the BiomedGT Semantic Media Wiki (SMW). A documentation wiki that provides the documentation for NPO is available at http://www.nano-ontology.org.

The ontology URI of NPO is http://purl.bioontology.org/ontology/npo

The NPO is also included in the NCI metathesaurus (NCIm), which can be accessed at http://ncimeta.nci.nih.gov/ .

The NCI metathesaurus contains about 3,600,000 terms from over 76 vocabularies, and these terms are mapped to about 1,400,000 biomedical concepts. Terms from multiple vocabularies that are mapped to a single biomedical concept allows the user to choose from the multiple vocabularies to annotate data. Simultaneously, this facilitates discovery of vocabularies unknown to the user. By the inclusion of NPO into the NCI metathesaurus, we expect that NPO accessibility and usage will be extended within the NCIm; NPO will add semantics into the NCIm; and that NCIm users will be able to take advantage of the knowledge provided by NPO.

Release Cycles

New versions of the NPO will be released every three months through the NCBO BioPortal and through the EVS NCI term browser. Release notes for the different versions will be made available through the documentation wiki (http://www.nano-ontology.org/).

Community Acceptance

There has been no formal acceptance of the NPO as a de facto standard by the communities yet. Currently, it is the only ontology designed specifically for the cancer nanotechnology domain in terms of its scope and purpose. It is a relatively new ontology compared to existing ontologies / CVs such as GO, ChEBI and NCIT, and NPO is more relevant for use by communities involved in cancer nanotechnology research, including developers and users of knowledge bases that capture nanomaterial data (e.g., caNanoLab and nano-TAB). Mechanisms for attaining community acceptance will be determined through the caBIG Nano WG activities, adoption and use of NPO in both caNanoLab and nano-TAB, and through the use of BiomedGT SMW which enables communities to collaborate together, evaluate NPO and contribute to NPO development.

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