lab

 

As a first example of the use of ChAMP in creation of a standard, research article metadata was chosen.  When we research the literature, we see that publishers provide keywords with the bibliographic information and the abstract on the page for the article.  While the keywords are important - they are what the papers' author(s) think are important facets of the research described - they are not standardized and thus do not really fit the needs of the readers of the paper.

In most cases, we find a paper via a text search of the title and abstract and then look for specific metadata (detection limit, analysis time, instrumentation, method accuracy, etc.) to evaluate whether it is something we can use, compare our work to, etc.  With that in mind, using ChAMP to represent important chemical analysis metadata (that researchers would like to search and compare methods with) is a logical use of the platform.

Starting from the ChAMP XML Schema any/all pieces of the schema can be used to create a schema for this application.  Below is an image of the schema for this example.  Remember, standards authors can design this any way they think is appropriate for their application.

[Other links:  ChAMP Standard Method XML ExampleChAMP Referemce Material XML Example]

 article schema

As you can see, the schema picks only certain elements for the standard.  It shows how to re-purpose existing elements ('champ:description') with a new name ('overview') using the 'substitutionGroup' attribute.  You can also import other schema, if you want a standard to use elements from schema other that ChAMP. Below is what an example XML file might look like representing the metadata about a specific paper.

article xml

Alternatively, the links to the ChAMP ontology can be added to the XML file as seen below

article xml ont

Either way, because the ChAMP XML schema is designed with the ontology references included, the metadata items can be crosswalked to the ontology by using the schema.

After developing the metadata categories and items that characterize chemical analysis it was time to turn to the development of an ontology for chemical analysis.  Development begin by reviewing the entries and organization structure of the following ontologies

As a resullt the Chemical Analysis Ontology (CAO) is organized using the BFO framework with entries primarily under concepts (not complete by any means), material entities, information content entities (data items), roles, and processes. Currently, the ontology is more of a vocabulary in that development of predicates (ontology properties) that relate subjects to objects has not been a focal point. This will be fleshed out over the summer of 2015.

Graphical snapshots of the  0.1 version are show below and the current version of the ontology (0.2 - 4/29/15) in RDF/OWL (using OWL-DL) is linked here.  Please feed any comments to This email address is being protected from spambots. You need JavaScript enabled to view it..

Material Entities

material entities

Concepts (need a lot of work)

concepts

Information Content Entities

data items

Roles

expanded roles

One of the common ways that scientists currently annotate research papers for peer-review publication is to a keywords, or better yet, concept terms.  While it is impractical for ChAMP to define lists of technique specific concept terms it should i) provide a generic set of concept terms for chemical analysis and ii) provide a mechanism for inclusion of more specific concepts from existing or future lists developed by technique experts (e.g. IUPAC Orange Book).  Send any comments to This email address is being protected from spambots. You need JavaScript enabled to view it..

  • concept: a particular concept in the context of a chemical analysis that helps to clarify important aspects of the methodology [02-17-15]
  • scope: the extent of applicability (in terms of analysis technique or chemical analysis) of the concept [02-17-15]
  • vocabulary: reference to a defined controlled vocabulary/ontology [02-17-15]

To contextualize the chemical analysis data it is important to identify the people involved, roles they play, and the places that they analysis was developed.

  • contact: a specific individual that can be contacted about the chemical analysis (string) [2-12-15]
  • person: an individual that has participated in part in the development/production/publication of the chemical analysis (string) [1-19-15]
  • organization: a company/institution/organization that was part of the development/production/publication of the chemical analysis (string) [1-19-15]
  • funding agency: a public or private group that was a source of funding relative to the chemical analysis (string) [1-19-15]
  • role: the part that a contact plays in the development/production/publication of the chemical analysis (string/enum) [1-19-15]
  • address: physical address identifying the location of a contact (string) [2-12-15]
  • phone: telephone number for communicating with a contact (string) [2-12-15]
  • email: electronic mailing address for communicating with a contact (string) [2-12-15]
  • location: a place where one or more activities was performed in the development/production/publication (e.g. building/lab) of the chemical analysis (string) [2-26-15]