SlideShare a Scribd company logo

Building a Standard for Standards: The ChAMP Project

Stuart Chalk
Stuart Chalk
Stuart ChalkAssociate Professor of Chemistry at University of North Florida

Building a Standard for Standards: The ChAMP Project

1 of 35
Download to read offline
Building a Standard for
Standards: The ChAMP project
(http://champ-project.org)
Stuart J. Chalk, Department of Chemistry, University of North Florida
Antony Williams and Valery Tkachenko, RSC Cheminformatics
schalk@unf.edu
ACS Meeting Denver 2015
 Initial Idea
 Motivation
 Why a Platform?
 Pieces of the Puzzle
 Existing Resources
 What are the Most Important Metadata?
 Minimum Information About a Chemical Analysis?
 Ontology Development
 Example Application(s)
 Future Developments
 Conclusion
Overview
 Develop a set of metadata items for
representation/annotation of chemical analysis
information
 Are there important characteristics (metadata) about
analysis methodologies that, if captured, would add
value to a resource?
 Must be easy to implement
 Must be useful across multiple disciplines
Initial Idea
 How to facilitate aggregation/searching of CA information?
 Knowledge in existing literature
 Annotation of research in future publications
 Annotation of (potentially useful) unpublished/self published work
 Annotation of data captured in ELN’s
 Need tool to annotate data in digital repositories
 Provide users with uniform (but flexible) mechanism to categorize
data they contribute
 Help researchers articulate data management plans in grants
 Complement/extend existing activities
 The haystack is so big – we need to make it easy to visualize the
needle by accurate annotation of available methodologies
Motivation
RSC Data Repository
 Look at the posts for analytical method help on Linked-In
 ‘I need an ICP-MS application note about direct determination
of sulfur and phosphate in microwave digested plant material
and soil without using external oxygen as a reaction gas.’ (ICP-
OES and ICP-MS)
 ‘I want to validate a method of detecting As in glass vials with
the aid of atomic absorption and air-acetylene flame’.
(Analytical Method Validation)
 ‘Does anyone know another method for determining total iron
and copper in water other than calorimeter and wet chemistry?’
(Analytical Chemistry)
 ‘Anyone with knowledge in electrochemical detection of
Homovanillic acid in urine samples?’ (Analytical Chemistry)
Motivation

Recommended

Clustering the royal society of chemistry chemical repository to enable enhan...
Clustering the royal society of chemistry chemical repository to enable enhan...Clustering the royal society of chemistry chemical repository to enable enhan...
Clustering the royal society of chemistry chemical repository to enable enhan...Valery Tkachenko
 
ACS 248th Paper 136 JSmol/JSpecView Eureka Integration
ACS 248th Paper 136 JSmol/JSpecView Eureka IntegrationACS 248th Paper 136 JSmol/JSpecView Eureka Integration
ACS 248th Paper 136 JSmol/JSpecView Eureka IntegrationStuart Chalk
 
ACS 248th Paper 71 ChAMP Project
ACS 248th Paper 71 ChAMP ProjectACS 248th Paper 71 ChAMP Project
ACS 248th Paper 71 ChAMP ProjectStuart Chalk
 
Building a semantic chemistry platform with the royal society of chemistry
Building a semantic chemistry platform with the royal society of chemistryBuilding a semantic chemistry platform with the royal society of chemistry
Building a semantic chemistry platform with the royal society of chemistryValery Tkachenko
 
Acs collaborative computational technologies for biomedical research an enabl...
Acs collaborative computational technologies for biomedical research an enabl...Acs collaborative computational technologies for biomedical research an enabl...
Acs collaborative computational technologies for biomedical research an enabl...Sean Ekins
 
The royal society of chemistry and its adoption of semantic web technologies ...
The royal society of chemistry and its adoption of semantic web technologies ...The royal society of chemistry and its adoption of semantic web technologies ...
The royal society of chemistry and its adoption of semantic web technologies ...Valery Tkachenko
 
Supporting the exploding dimensions of the chemical sciences via global netwo...
Supporting the exploding dimensions of the chemical sciences via global netwo...Supporting the exploding dimensions of the chemical sciences via global netwo...
Supporting the exploding dimensions of the chemical sciences via global netwo...Valery Tkachenko
 

More Related Content

What's hot

FAIR Data and Model Management for Systems Biology (and SOPs too!)
FAIR Data and Model Management for Systems Biology(and SOPs too!)FAIR Data and Model Management for Systems Biology(and SOPs too!)
FAIR Data and Model Management for Systems Biology (and SOPs too!)Carole Goble
 
Improving the Management of Computational Models -- Invited talk at the EBI
Improving the Management of Computational Models -- Invited talk at the EBIImproving the Management of Computational Models -- Invited talk at the EBI
Improving the Management of Computational Models -- Invited talk at the EBIMartin Scharm
 
Tools and approaches for data deposition into nanomaterial databases
Tools and approaches for data deposition into nanomaterial databasesTools and approaches for data deposition into nanomaterial databases
Tools and approaches for data deposition into nanomaterial databasesValery Tkachenko
 
Opportunities in chemical structure standardization
Opportunities in chemical structure standardizationOpportunities in chemical structure standardization
Opportunities in chemical structure standardizationValery Tkachenko
 
Enhancing the Quality of ImmPort Data
Enhancing the Quality of ImmPort DataEnhancing the Quality of ImmPort Data
Enhancing the Quality of ImmPort DataBarry Smith
 
Chemistry Validation and Standardization Platform v2.0
Chemistry Validation and Standardization Platform v2.0Chemistry Validation and Standardization Platform v2.0
Chemistry Validation and Standardization Platform v2.0Valery Tkachenko
 
FAIR Data, Operations and Model management for Systems Biology and Systems Me...
FAIR Data, Operations and Model management for Systems Biology and Systems Me...FAIR Data, Operations and Model management for Systems Biology and Systems Me...
FAIR Data, Operations and Model management for Systems Biology and Systems Me...Carole Goble
 
Facilitating semantic alignment.-biohackathon-jupp
Facilitating semantic alignment.-biohackathon-juppFacilitating semantic alignment.-biohackathon-jupp
Facilitating semantic alignment.-biohackathon-juppSimon Jupp
 
schema.org and biomedical ontologies
schema.org and biomedical ontologies schema.org and biomedical ontologies
schema.org and biomedical ontologies Simon Jupp
 
eXframe: A Semantic Web Platform for Genomic Experiments
eXframe: A Semantic Web Platform for Genomic ExperimentseXframe: A Semantic Web Platform for Genomic Experiments
eXframe: A Semantic Web Platform for Genomic ExperimentsTim Clark
 
exFrame: a Semantic Web Platform for Genomics Experiments
exFrame: a Semantic Web Platform for Genomics ExperimentsexFrame: a Semantic Web Platform for Genomics Experiments
exFrame: a Semantic Web Platform for Genomics ExperimentsTim Clark
 
Citing data in research articles: principles, implementation, challenges - an...
Citing data in research articles: principles, implementation, challenges - an...Citing data in research articles: principles, implementation, challenges - an...
Citing data in research articles: principles, implementation, challenges - an...FAIRDOM
 
Annotopia open annotation services platform
Annotopia open annotation services platformAnnotopia open annotation services platform
Annotopia open annotation services platformTim Clark
 
Standardization of the HIPC Data Templates: The Story So Far
Standardization of the HIPC Data Templates: The Story So FarStandardization of the HIPC Data Templates: The Story So Far
Standardization of the HIPC Data Templates: The Story So FarAhmad C. Bukhari
 
Open Science Data Repository - the platform for materials research
Open Science Data Repository - the platform for materials researchOpen Science Data Repository - the platform for materials research
Open Science Data Repository - the platform for materials researchValery Tkachenko
 

What's hot (20)

FAIR Data and Model Management for Systems Biology (and SOPs too!)
FAIR Data and Model Management for Systems Biology(and SOPs too!)FAIR Data and Model Management for Systems Biology(and SOPs too!)
FAIR Data and Model Management for Systems Biology (and SOPs too!)
 
Improving the Management of Computational Models -- Invited talk at the EBI
Improving the Management of Computational Models -- Invited talk at the EBIImproving the Management of Computational Models -- Invited talk at the EBI
Improving the Management of Computational Models -- Invited talk at the EBI
 
Tools and approaches for data deposition into nanomaterial databases
Tools and approaches for data deposition into nanomaterial databasesTools and approaches for data deposition into nanomaterial databases
Tools and approaches for data deposition into nanomaterial databases
 
Opportunities in chemical structure standardization
Opportunities in chemical structure standardizationOpportunities in chemical structure standardization
Opportunities in chemical structure standardization
 
Enhancing the Quality of ImmPort Data
Enhancing the Quality of ImmPort DataEnhancing the Quality of ImmPort Data
Enhancing the Quality of ImmPort Data
 
Chemistry Validation and Standardization Platform v2.0
Chemistry Validation and Standardization Platform v2.0Chemistry Validation and Standardization Platform v2.0
Chemistry Validation and Standardization Platform v2.0
 
FAIR Data, Operations and Model management for Systems Biology and Systems Me...
FAIR Data, Operations and Model management for Systems Biology and Systems Me...FAIR Data, Operations and Model management for Systems Biology and Systems Me...
FAIR Data, Operations and Model management for Systems Biology and Systems Me...
 
The UK National Chemical Database Service – an integration of commercial and ...
The UK National Chemical Database Service – an integration of commercial and ...The UK National Chemical Database Service – an integration of commercial and ...
The UK National Chemical Database Service – an integration of commercial and ...
 
Royal society of chemistry activities to develop a data repository for chemis...
Royal society of chemistry activities to develop a data repository for chemis...Royal society of chemistry activities to develop a data repository for chemis...
Royal society of chemistry activities to develop a data repository for chemis...
 
Facilitating semantic alignment.-biohackathon-jupp
Facilitating semantic alignment.-biohackathon-juppFacilitating semantic alignment.-biohackathon-jupp
Facilitating semantic alignment.-biohackathon-jupp
 
schema.org and biomedical ontologies
schema.org and biomedical ontologies schema.org and biomedical ontologies
schema.org and biomedical ontologies
 
eXframe: A Semantic Web Platform for Genomic Experiments
eXframe: A Semantic Web Platform for Genomic ExperimentseXframe: A Semantic Web Platform for Genomic Experiments
eXframe: A Semantic Web Platform for Genomic Experiments
 
exFrame: a Semantic Web Platform for Genomics Experiments
exFrame: a Semantic Web Platform for Genomics ExperimentsexFrame: a Semantic Web Platform for Genomics Experiments
exFrame: a Semantic Web Platform for Genomics Experiments
 
Citing data in research articles: principles, implementation, challenges - an...
Citing data in research articles: principles, implementation, challenges - an...Citing data in research articles: principles, implementation, challenges - an...
Citing data in research articles: principles, implementation, challenges - an...
 
ROHub
ROHubROHub
ROHub
 
An Open Repository Model for Acquiring Knowledge About Scientific Experiments
An Open Repository Model for Acquiring Knowledge About Scientific ExperimentsAn Open Repository Model for Acquiring Knowledge About Scientific Experiments
An Open Repository Model for Acquiring Knowledge About Scientific Experiments
 
Annotopia open annotation services platform
Annotopia open annotation services platformAnnotopia open annotation services platform
Annotopia open annotation services platform
 
The importance of standards for data exchange and interchange on the Royal So...
The importance of standards for data exchange and interchange on the Royal So...The importance of standards for data exchange and interchange on the Royal So...
The importance of standards for data exchange and interchange on the Royal So...
 
Standardization of the HIPC Data Templates: The Story So Far
Standardization of the HIPC Data Templates: The Story So FarStandardization of the HIPC Data Templates: The Story So Far
Standardization of the HIPC Data Templates: The Story So Far
 
Open Science Data Repository - the platform for materials research
Open Science Data Repository - the platform for materials researchOpen Science Data Repository - the platform for materials research
Open Science Data Repository - the platform for materials research
 

Similar to Building a Standard for Standards: The ChAMP Project

Symmetry 13-00195-v2
Symmetry 13-00195-v2Symmetry 13-00195-v2
Symmetry 13-00195-v2AdamsOdanji
 
Being FAIR: FAIR data and model management SSBSS 2017 Summer School
Being FAIR:  FAIR data and model management SSBSS 2017 Summer SchoolBeing FAIR:  FAIR data and model management SSBSS 2017 Summer School
Being FAIR: FAIR data and model management SSBSS 2017 Summer SchoolCarole Goble
 
Medinfo 2010 openEHR Clinical Modelling Worshop
Medinfo 2010 openEHR Clinical Modelling WorshopMedinfo 2010 openEHR Clinical Modelling Worshop
Medinfo 2010 openEHR Clinical Modelling WorshopKoray Atalag
 
Preservation Planning using Plato, by Hannes Kulovits and Andreas Rauber
Preservation Planning using Plato, by Hannes Kulovits and Andreas RauberPreservation Planning using Plato, by Hannes Kulovits and Andreas Rauber
Preservation Planning using Plato, by Hannes Kulovits and Andreas RauberJISC KeepIt project
 
Semantics for integrated laboratory analytical processes - The Allotrope Pers...
Semantics for integrated laboratory analytical processes - The Allotrope Pers...Semantics for integrated laboratory analytical processes - The Allotrope Pers...
Semantics for integrated laboratory analytical processes - The Allotrope Pers...OSTHUS
 
Clinical modelling with openEHR Archetypes
Clinical modelling with openEHR ArchetypesClinical modelling with openEHR Archetypes
Clinical modelling with openEHR ArchetypesKoray Atalag
 
Methodology and Campaign Design for the Evaluation of Semantic Search Tools
Methodology and Campaign Design for the Evaluation of Semantic Search ToolsMethodology and Campaign Design for the Evaluation of Semantic Search Tools
Methodology and Campaign Design for the Evaluation of Semantic Search ToolsStuart Wrigley
 
Curation-Friendly Tools for the Scientific Researcher
Curation-Friendly Tools for the Scientific ResearcherCuration-Friendly Tools for the Scientific Researcher
Curation-Friendly Tools for the Scientific Researcherbwestra
 
Metagenomic Data Provenance and Management using the ISA infrastructure --- o...
Metagenomic Data Provenance and Management using the ISA infrastructure --- o...Metagenomic Data Provenance and Management using the ISA infrastructure --- o...
Metagenomic Data Provenance and Management using the ISA infrastructure --- o...Alejandra Gonzalez-Beltran
 
Metabolomic Data Analysis Workshop and Tutorials (2014)
Metabolomic Data Analysis Workshop and Tutorials (2014)Metabolomic Data Analysis Workshop and Tutorials (2014)
Metabolomic Data Analysis Workshop and Tutorials (2014)Dmitry Grapov
 
2006-03-21 Work Group Meeting on IT Techniques, Tools and Philosophies for Mo...
2006-03-21 Work Group Meeting on IT Techniques, Tools and Philosophies for Mo...2006-03-21 Work Group Meeting on IT Techniques, Tools and Philosophies for Mo...
2006-03-21 Work Group Meeting on IT Techniques, Tools and Philosophies for Mo...Rudolf Husar
 
Exploratory Factor Analysis; Concepts and Theory
Exploratory Factor Analysis; Concepts and TheoryExploratory Factor Analysis; Concepts and Theory
Exploratory Factor Analysis; Concepts and TheoryHamed Taherdoost
 
SDTM (Study Data Tabulation Model)
SDTM (Study Data Tabulation Model)SDTM (Study Data Tabulation Model)
SDTM (Study Data Tabulation Model)SWAROOP KUMAR K
 
Driving Deep Semantics in Middleware and Networks: What, why and how?
Driving Deep Semantics in Middleware and Networks: What, why and how?Driving Deep Semantics in Middleware and Networks: What, why and how?
Driving Deep Semantics in Middleware and Networks: What, why and how?Amit Sheth
 
Writing a scientific manuscript
Writing a scientific manuscriptWriting a scientific manuscript
Writing a scientific manuscriptMartin McMorrow
 

Similar to Building a Standard for Standards: The ChAMP Project (20)

Symmetry 13-00195-v2
Symmetry 13-00195-v2Symmetry 13-00195-v2
Symmetry 13-00195-v2
 
Being FAIR: FAIR data and model management SSBSS 2017 Summer School
Being FAIR:  FAIR data and model management SSBSS 2017 Summer SchoolBeing FAIR:  FAIR data and model management SSBSS 2017 Summer School
Being FAIR: FAIR data and model management SSBSS 2017 Summer School
 
The Chemtools LaBLog
The Chemtools LaBLogThe Chemtools LaBLog
The Chemtools LaBLog
 
Medinfo 2010 openEHR Clinical Modelling Worshop
Medinfo 2010 openEHR Clinical Modelling WorshopMedinfo 2010 openEHR Clinical Modelling Worshop
Medinfo 2010 openEHR Clinical Modelling Worshop
 
Preservation Planning using Plato, by Hannes Kulovits and Andreas Rauber
Preservation Planning using Plato, by Hannes Kulovits and Andreas RauberPreservation Planning using Plato, by Hannes Kulovits and Andreas Rauber
Preservation Planning using Plato, by Hannes Kulovits and Andreas Rauber
 
Semantics for integrated laboratory analytical processes - The Allotrope Pers...
Semantics for integrated laboratory analytical processes - The Allotrope Pers...Semantics for integrated laboratory analytical processes - The Allotrope Pers...
Semantics for integrated laboratory analytical processes - The Allotrope Pers...
 
Clinical modelling with openEHR Archetypes
Clinical modelling with openEHR ArchetypesClinical modelling with openEHR Archetypes
Clinical modelling with openEHR Archetypes
 
Bibliographic metadata (including citation)
Bibliographic metadata (including citation)Bibliographic metadata (including citation)
Bibliographic metadata (including citation)
 
Methodology and Campaign Design for the Evaluation of Semantic Search Tools
Methodology and Campaign Design for the Evaluation of Semantic Search ToolsMethodology and Campaign Design for the Evaluation of Semantic Search Tools
Methodology and Campaign Design for the Evaluation of Semantic Search Tools
 
Curation-Friendly Tools for the Scientific Researcher
Curation-Friendly Tools for the Scientific ResearcherCuration-Friendly Tools for the Scientific Researcher
Curation-Friendly Tools for the Scientific Researcher
 
Metagenomic Data Provenance and Management using the ISA infrastructure --- o...
Metagenomic Data Provenance and Management using the ISA infrastructure --- o...Metagenomic Data Provenance and Management using the ISA infrastructure --- o...
Metagenomic Data Provenance and Management using the ISA infrastructure --- o...
 
Metabolomic Data Analysis Workshop and Tutorials (2014)
Metabolomic Data Analysis Workshop and Tutorials (2014)Metabolomic Data Analysis Workshop and Tutorials (2014)
Metabolomic Data Analysis Workshop and Tutorials (2014)
 
2006-03-21 Work Group Meeting on IT Techniques, Tools and Philosophies for Mo...
2006-03-21 Work Group Meeting on IT Techniques, Tools and Philosophies for Mo...2006-03-21 Work Group Meeting on IT Techniques, Tools and Philosophies for Mo...
2006-03-21 Work Group Meeting on IT Techniques, Tools and Philosophies for Mo...
 
BioSD Tutorial 2014 Editition
BioSD Tutorial 2014 EdititionBioSD Tutorial 2014 Editition
BioSD Tutorial 2014 Editition
 
Introduction to SDTM
Introduction to SDTMIntroduction to SDTM
Introduction to SDTM
 
SETAC HTS SFlood
SETAC HTS SFlood SETAC HTS SFlood
SETAC HTS SFlood
 
Exploratory Factor Analysis; Concepts and Theory
Exploratory Factor Analysis; Concepts and TheoryExploratory Factor Analysis; Concepts and Theory
Exploratory Factor Analysis; Concepts and Theory
 
SDTM (Study Data Tabulation Model)
SDTM (Study Data Tabulation Model)SDTM (Study Data Tabulation Model)
SDTM (Study Data Tabulation Model)
 
Driving Deep Semantics in Middleware and Networks: What, why and how?
Driving Deep Semantics in Middleware and Networks: What, why and how?Driving Deep Semantics in Middleware and Networks: What, why and how?
Driving Deep Semantics in Middleware and Networks: What, why and how?
 
Writing a scientific manuscript
Writing a scientific manuscriptWriting a scientific manuscript
Writing a scientific manuscript
 

More from Stuart Chalk

Semantic properties and units
Semantic properties and unitsSemantic properties and units
Semantic properties and unitsStuart Chalk
 
Open semantic chemical structures
Open semantic chemical structuresOpen semantic chemical structures
Open semantic chemical structuresStuart Chalk
 
ChemExtractor: Enhanced Rule-Based Capture and Identification of PDF Based Pr...
ChemExtractor: Enhanced Rule-Based Capture and Identification of PDF Based Pr...ChemExtractor: Enhanced Rule-Based Capture and Identification of PDF Based Pr...
ChemExtractor: Enhanced Rule-Based Capture and Identification of PDF Based Pr...Stuart Chalk
 
AnIML: A New Analytical Data Standard
AnIML: A New Analytical Data StandardAnIML: A New Analytical Data Standard
AnIML: A New Analytical Data StandardStuart Chalk
 
A Generic Scientific Data Model and Ontology for Representation of Chemical Data
A Generic Scientific Data Model and Ontology for Representation of Chemical DataA Generic Scientific Data Model and Ontology for Representation of Chemical Data
A Generic Scientific Data Model and Ontology for Representation of Chemical DataStuart Chalk
 
Scientific Units in the Electronic Age
Scientific Units in the Electronic AgeScientific Units in the Electronic Age
Scientific Units in the Electronic AgeStuart Chalk
 
Toward Semantic Representation of Science in Electronic Laboratory Notebooks ...
Toward Semantic Representation of Science in Electronic Laboratory Notebooks ...Toward Semantic Representation of Science in Electronic Laboratory Notebooks ...
Toward Semantic Representation of Science in Electronic Laboratory Notebooks ...Stuart Chalk
 
Rule-based Capture/Storage of Scientific Data from PDF Files and Export using...
Rule-based Capture/Storage of Scientific Data from PDF Files and Export using...Rule-based Capture/Storage of Scientific Data from PDF Files and Export using...
Rule-based Capture/Storage of Scientific Data from PDF Files and Export using...Stuart Chalk
 
The Electronic Notebook Ontology
The Electronic Notebook OntologyThe Electronic Notebook Ontology
The Electronic Notebook OntologyStuart Chalk
 
Sharing Science Data: Semantically Reimagining the IUPAC Solubility Series Data
Sharing Science Data: Semantically Reimagining the IUPAC Solubility Series DataSharing Science Data: Semantically Reimagining the IUPAC Solubility Series Data
Sharing Science Data: Semantically Reimagining the IUPAC Solubility Series DataStuart Chalk
 
Bringing Flow injection Analysis to the Semantic Web
Bringing Flow injection Analysis to the Semantic WebBringing Flow injection Analysis to the Semantic Web
Bringing Flow injection Analysis to the Semantic WebStuart Chalk
 
Reactions to the Open Spectral Database
Reactions to the Open Spectral DatabaseReactions to the Open Spectral Database
Reactions to the Open Spectral DatabaseStuart Chalk
 
Integrating AnIML Files in Electronic Laboratory Notebooks - PittCon 2015
Integrating AnIML Files in Electronic Laboratory Notebooks - PittCon 2015Integrating AnIML Files in Electronic Laboratory Notebooks - PittCon 2015
Integrating AnIML Files in Electronic Laboratory Notebooks - PittCon 2015Stuart Chalk
 
A Standard Data Format for Computational Chemistry: CSX
A Standard Data Format for Computational Chemistry: CSXA Standard Data Format for Computational Chemistry: CSX
A Standard Data Format for Computational Chemistry: CSXStuart Chalk
 
Overview of the Analytical Information Markup Language (AnIML)
Overview of the Analytical Information Markup Language (AnIML)Overview of the Analytical Information Markup Language (AnIML)
Overview of the Analytical Information Markup Language (AnIML)Stuart Chalk
 
ACS 248th Paper 146 VIVO/ScientistsDB Integration into Eureka
ACS 248th Paper 146 VIVO/ScientistsDB Integration into EurekaACS 248th Paper 146 VIVO/ScientistsDB Integration into Eureka
ACS 248th Paper 146 VIVO/ScientistsDB Integration into EurekaStuart Chalk
 
ACS 248th Paper 108 NIST-IUPAC Solubility Data
ACS 248th Paper 108 NIST-IUPAC Solubility DataACS 248th Paper 108 NIST-IUPAC Solubility Data
ACS 248th Paper 108 NIST-IUPAC Solubility DataStuart Chalk
 
ACS 248th Paper 104 ChemData Project
ACS 248th Paper 104 ChemData ProjectACS 248th Paper 104 ChemData Project
ACS 248th Paper 104 ChemData ProjectStuart Chalk
 
ACS 248th Paper 67 Eureka Collaboration
ACS 248th Paper 67 Eureka CollaborationACS 248th Paper 67 Eureka Collaboration
ACS 248th Paper 67 Eureka CollaborationStuart Chalk
 
247th ACS Meeting: The Eureka Research Workbench
247th ACS Meeting: The Eureka Research Workbench247th ACS Meeting: The Eureka Research Workbench
247th ACS Meeting: The Eureka Research WorkbenchStuart Chalk
 

More from Stuart Chalk (20)

Semantic properties and units
Semantic properties and unitsSemantic properties and units
Semantic properties and units
 
Open semantic chemical structures
Open semantic chemical structuresOpen semantic chemical structures
Open semantic chemical structures
 
ChemExtractor: Enhanced Rule-Based Capture and Identification of PDF Based Pr...
ChemExtractor: Enhanced Rule-Based Capture and Identification of PDF Based Pr...ChemExtractor: Enhanced Rule-Based Capture and Identification of PDF Based Pr...
ChemExtractor: Enhanced Rule-Based Capture and Identification of PDF Based Pr...
 
AnIML: A New Analytical Data Standard
AnIML: A New Analytical Data StandardAnIML: A New Analytical Data Standard
AnIML: A New Analytical Data Standard
 
A Generic Scientific Data Model and Ontology for Representation of Chemical Data
A Generic Scientific Data Model and Ontology for Representation of Chemical DataA Generic Scientific Data Model and Ontology for Representation of Chemical Data
A Generic Scientific Data Model and Ontology for Representation of Chemical Data
 
Scientific Units in the Electronic Age
Scientific Units in the Electronic AgeScientific Units in the Electronic Age
Scientific Units in the Electronic Age
 
Toward Semantic Representation of Science in Electronic Laboratory Notebooks ...
Toward Semantic Representation of Science in Electronic Laboratory Notebooks ...Toward Semantic Representation of Science in Electronic Laboratory Notebooks ...
Toward Semantic Representation of Science in Electronic Laboratory Notebooks ...
 
Rule-based Capture/Storage of Scientific Data from PDF Files and Export using...
Rule-based Capture/Storage of Scientific Data from PDF Files and Export using...Rule-based Capture/Storage of Scientific Data from PDF Files and Export using...
Rule-based Capture/Storage of Scientific Data from PDF Files and Export using...
 
The Electronic Notebook Ontology
The Electronic Notebook OntologyThe Electronic Notebook Ontology
The Electronic Notebook Ontology
 
Sharing Science Data: Semantically Reimagining the IUPAC Solubility Series Data
Sharing Science Data: Semantically Reimagining the IUPAC Solubility Series DataSharing Science Data: Semantically Reimagining the IUPAC Solubility Series Data
Sharing Science Data: Semantically Reimagining the IUPAC Solubility Series Data
 
Bringing Flow injection Analysis to the Semantic Web
Bringing Flow injection Analysis to the Semantic WebBringing Flow injection Analysis to the Semantic Web
Bringing Flow injection Analysis to the Semantic Web
 
Reactions to the Open Spectral Database
Reactions to the Open Spectral DatabaseReactions to the Open Spectral Database
Reactions to the Open Spectral Database
 
Integrating AnIML Files in Electronic Laboratory Notebooks - PittCon 2015
Integrating AnIML Files in Electronic Laboratory Notebooks - PittCon 2015Integrating AnIML Files in Electronic Laboratory Notebooks - PittCon 2015
Integrating AnIML Files in Electronic Laboratory Notebooks - PittCon 2015
 
A Standard Data Format for Computational Chemistry: CSX
A Standard Data Format for Computational Chemistry: CSXA Standard Data Format for Computational Chemistry: CSX
A Standard Data Format for Computational Chemistry: CSX
 
Overview of the Analytical Information Markup Language (AnIML)
Overview of the Analytical Information Markup Language (AnIML)Overview of the Analytical Information Markup Language (AnIML)
Overview of the Analytical Information Markup Language (AnIML)
 
ACS 248th Paper 146 VIVO/ScientistsDB Integration into Eureka
ACS 248th Paper 146 VIVO/ScientistsDB Integration into EurekaACS 248th Paper 146 VIVO/ScientistsDB Integration into Eureka
ACS 248th Paper 146 VIVO/ScientistsDB Integration into Eureka
 
ACS 248th Paper 108 NIST-IUPAC Solubility Data
ACS 248th Paper 108 NIST-IUPAC Solubility DataACS 248th Paper 108 NIST-IUPAC Solubility Data
ACS 248th Paper 108 NIST-IUPAC Solubility Data
 
ACS 248th Paper 104 ChemData Project
ACS 248th Paper 104 ChemData ProjectACS 248th Paper 104 ChemData Project
ACS 248th Paper 104 ChemData Project
 
ACS 248th Paper 67 Eureka Collaboration
ACS 248th Paper 67 Eureka CollaborationACS 248th Paper 67 Eureka Collaboration
ACS 248th Paper 67 Eureka Collaboration
 
247th ACS Meeting: The Eureka Research Workbench
247th ACS Meeting: The Eureka Research Workbench247th ACS Meeting: The Eureka Research Workbench
247th ACS Meeting: The Eureka Research Workbench
 

Recently uploaded

Thornyissue testing of slideshow for website
Thornyissue testing of slideshow for websiteThornyissue testing of slideshow for website
Thornyissue testing of slideshow for websitesuelcarter1
 
PROSTHETIC FEET description and its types
PROSTHETIC FEET description and its typesPROSTHETIC FEET description and its types
PROSTHETIC FEET description and its typeseshasmalik27
 
Pineal region.pptx
Pineal region.pptxPineal region.pptx
Pineal region.pptxRunBalaB
 
Fair and just food systems enabling local midstream businesses? What does it ...
Fair and just food systems enabling local midstream businesses? What does it ...Fair and just food systems enabling local midstream businesses? What does it ...
Fair and just food systems enabling local midstream businesses? What does it ...SIANI
 
A seven-Earth-radius helium-burning star inside a 20.5-min detached binary
A seven-Earth-radius helium-burning star inside a 20.5-min detached binaryA seven-Earth-radius helium-burning star inside a 20.5-min detached binary
A seven-Earth-radius helium-burning star inside a 20.5-min detached binarySérgio Sacani
 
Open Access Publishing and the Open Journal of Astrophysics
Open Access Publishing and the Open Journal of AstrophysicsOpen Access Publishing and the Open Journal of Astrophysics
Open Access Publishing and the Open Journal of AstrophysicsPeter Coles
 
ROLES OF MICROBES IN BIOCONTROL BY ANKIT CHOUDHARY.ppsx
ROLES OF MICROBES IN BIOCONTROL BY ANKIT CHOUDHARY.ppsxROLES OF MICROBES IN BIOCONTROL BY ANKIT CHOUDHARY.ppsx
ROLES OF MICROBES IN BIOCONTROL BY ANKIT CHOUDHARY.ppsxAnkitChoudhary955647
 
Carpal tunnel Syndrom Wesam Aljabali -1.pdf
Carpal tunnel Syndrom Wesam Aljabali -1.pdfCarpal tunnel Syndrom Wesam Aljabali -1.pdf
Carpal tunnel Syndrom Wesam Aljabali -1.pdfMsm_mo
 
Introduction to the research of stem cells
Introduction to the research of stem cellsIntroduction to the research of stem cells
Introduction to the research of stem cellsAlaaOraby6
 
dkNET Webinar: An Encyclopedia of the Adipose Tissue Secretome to Identify Me...
dkNET Webinar: An Encyclopedia of the Adipose Tissue Secretome to Identify Me...dkNET Webinar: An Encyclopedia of the Adipose Tissue Secretome to Identify Me...
dkNET Webinar: An Encyclopedia of the Adipose Tissue Secretome to Identify Me...dkNET
 
Advancing CAM Assay Image Analysis Using Deep Learning Software
Advancing CAM Assay Image Analysis Using Deep Learning SoftwareAdvancing CAM Assay Image Analysis Using Deep Learning Software
Advancing CAM Assay Image Analysis Using Deep Learning SoftwareKML Vision
 
FINAL Shehnaz and Thane Interview PowerPoint ;-).pdf
FINAL Shehnaz and Thane Interview PowerPoint ;-).pdfFINAL Shehnaz and Thane Interview PowerPoint ;-).pdf
FINAL Shehnaz and Thane Interview PowerPoint ;-).pdfThane Heins
 
ELK ELISA Kits Manufacturer in Singapore
ELK ELISA Kits Manufacturer in SingaporeELK ELISA Kits Manufacturer in Singapore
ELK ELISA Kits Manufacturer in SingaporeGaia Science Pte Ltd
 
Blood parasites (1).ppt parasitology zoology
Blood parasites (1).ppt parasitology zoologyBlood parasites (1).ppt parasitology zoology
Blood parasites (1).ppt parasitology zoologyssuser4d911a
 
Physics Chapter Three - Electric Fields and Charges
Physics Chapter Three - Electric Fields and ChargesPhysics Chapter Three - Electric Fields and Charges
Physics Chapter Three - Electric Fields and Chargesalinford
 
Agroecology as an approach to design sustainable Food Systems
Agroecology as an approach to design sustainable Food SystemsAgroecology as an approach to design sustainable Food Systems
Agroecology as an approach to design sustainable Food SystemsSIANI
 
An Introduction to Quantum Programming Languages
An Introduction to Quantum Programming LanguagesAn Introduction to Quantum Programming Languages
An Introduction to Quantum Programming LanguagesDavid Yonge-Mallo
 
Geological evidence of extensive N-fixation by volcanic lightning during very...
Geological evidence of extensive N-fixation by volcanic lightning during very...Geological evidence of extensive N-fixation by volcanic lightning during very...
Geological evidence of extensive N-fixation by volcanic lightning during very...Sérgio Sacani
 

Recently uploaded (20)

Thornyissue testing of slideshow for website
Thornyissue testing of slideshow for websiteThornyissue testing of slideshow for website
Thornyissue testing of slideshow for website
 
PROSTHETIC FEET description and its types
PROSTHETIC FEET description and its typesPROSTHETIC FEET description and its types
PROSTHETIC FEET description and its types
 
Pineal region.pptx
Pineal region.pptxPineal region.pptx
Pineal region.pptx
 
Fair and just food systems enabling local midstream businesses? What does it ...
Fair and just food systems enabling local midstream businesses? What does it ...Fair and just food systems enabling local midstream businesses? What does it ...
Fair and just food systems enabling local midstream businesses? What does it ...
 
A seven-Earth-radius helium-burning star inside a 20.5-min detached binary
A seven-Earth-radius helium-burning star inside a 20.5-min detached binaryA seven-Earth-radius helium-burning star inside a 20.5-min detached binary
A seven-Earth-radius helium-burning star inside a 20.5-min detached binary
 
ALL the evidence webinar: Appraising and using evidence about community conte...
ALL the evidence webinar: Appraising and using evidence about community conte...ALL the evidence webinar: Appraising and using evidence about community conte...
ALL the evidence webinar: Appraising and using evidence about community conte...
 
Open Access Publishing and the Open Journal of Astrophysics
Open Access Publishing and the Open Journal of AstrophysicsOpen Access Publishing and the Open Journal of Astrophysics
Open Access Publishing and the Open Journal of Astrophysics
 
ROLES OF MICROBES IN BIOCONTROL BY ANKIT CHOUDHARY.ppsx
ROLES OF MICROBES IN BIOCONTROL BY ANKIT CHOUDHARY.ppsxROLES OF MICROBES IN BIOCONTROL BY ANKIT CHOUDHARY.ppsx
ROLES OF MICROBES IN BIOCONTROL BY ANKIT CHOUDHARY.ppsx
 
Carpal tunnel Syndrom Wesam Aljabali -1.pdf
Carpal tunnel Syndrom Wesam Aljabali -1.pdfCarpal tunnel Syndrom Wesam Aljabali -1.pdf
Carpal tunnel Syndrom Wesam Aljabali -1.pdf
 
VEM 023- LESSON 1.pdf
VEM 023- LESSON 1.pdfVEM 023- LESSON 1.pdf
VEM 023- LESSON 1.pdf
 
Introduction to the research of stem cells
Introduction to the research of stem cellsIntroduction to the research of stem cells
Introduction to the research of stem cells
 
dkNET Webinar: An Encyclopedia of the Adipose Tissue Secretome to Identify Me...
dkNET Webinar: An Encyclopedia of the Adipose Tissue Secretome to Identify Me...dkNET Webinar: An Encyclopedia of the Adipose Tissue Secretome to Identify Me...
dkNET Webinar: An Encyclopedia of the Adipose Tissue Secretome to Identify Me...
 
Advancing CAM Assay Image Analysis Using Deep Learning Software
Advancing CAM Assay Image Analysis Using Deep Learning SoftwareAdvancing CAM Assay Image Analysis Using Deep Learning Software
Advancing CAM Assay Image Analysis Using Deep Learning Software
 
FINAL Shehnaz and Thane Interview PowerPoint ;-).pdf
FINAL Shehnaz and Thane Interview PowerPoint ;-).pdfFINAL Shehnaz and Thane Interview PowerPoint ;-).pdf
FINAL Shehnaz and Thane Interview PowerPoint ;-).pdf
 
ELK ELISA Kits Manufacturer in Singapore
ELK ELISA Kits Manufacturer in SingaporeELK ELISA Kits Manufacturer in Singapore
ELK ELISA Kits Manufacturer in Singapore
 
Blood parasites (1).ppt parasitology zoology
Blood parasites (1).ppt parasitology zoologyBlood parasites (1).ppt parasitology zoology
Blood parasites (1).ppt parasitology zoology
 
Physics Chapter Three - Electric Fields and Charges
Physics Chapter Three - Electric Fields and ChargesPhysics Chapter Three - Electric Fields and Charges
Physics Chapter Three - Electric Fields and Charges
 
Agroecology as an approach to design sustainable Food Systems
Agroecology as an approach to design sustainable Food SystemsAgroecology as an approach to design sustainable Food Systems
Agroecology as an approach to design sustainable Food Systems
 
An Introduction to Quantum Programming Languages
An Introduction to Quantum Programming LanguagesAn Introduction to Quantum Programming Languages
An Introduction to Quantum Programming Languages
 
Geological evidence of extensive N-fixation by volcanic lightning during very...
Geological evidence of extensive N-fixation by volcanic lightning during very...Geological evidence of extensive N-fixation by volcanic lightning during very...
Geological evidence of extensive N-fixation by volcanic lightning during very...
 

Building a Standard for Standards: The ChAMP Project

  • 1. Building a Standard for Standards: The ChAMP project (http://champ-project.org) Stuart J. Chalk, Department of Chemistry, University of North Florida Antony Williams and Valery Tkachenko, RSC Cheminformatics schalk@unf.edu ACS Meeting Denver 2015
  • 2.  Initial Idea  Motivation  Why a Platform?  Pieces of the Puzzle  Existing Resources  What are the Most Important Metadata?  Minimum Information About a Chemical Analysis?  Ontology Development  Example Application(s)  Future Developments  Conclusion Overview
  • 3.  Develop a set of metadata items for representation/annotation of chemical analysis information  Are there important characteristics (metadata) about analysis methodologies that, if captured, would add value to a resource?  Must be easy to implement  Must be useful across multiple disciplines Initial Idea
  • 4.  How to facilitate aggregation/searching of CA information?  Knowledge in existing literature  Annotation of research in future publications  Annotation of (potentially useful) unpublished/self published work  Annotation of data captured in ELN’s  Need tool to annotate data in digital repositories  Provide users with uniform (but flexible) mechanism to categorize data they contribute  Help researchers articulate data management plans in grants  Complement/extend existing activities  The haystack is so big – we need to make it easy to visualize the needle by accurate annotation of available methodologies Motivation
  • 6.  Look at the posts for analytical method help on Linked-In  ‘I need an ICP-MS application note about direct determination of sulfur and phosphate in microwave digested plant material and soil without using external oxygen as a reaction gas.’ (ICP- OES and ICP-MS)  ‘I want to validate a method of detecting As in glass vials with the aid of atomic absorption and air-acetylene flame’. (Analytical Method Validation)  ‘Does anyone know another method for determining total iron and copper in water other than calorimeter and wet chemistry?’ (Analytical Chemistry)  ‘Anyone with knowledge in electrochemical detection of Homovanillic acid in urine samples?’ (Analytical Chemistry) Motivation
  • 7.  Develop it to be as broadly applicable as possible  Chemical analysis is a not tangible like a spectrum  Users have domain specific needs/goals  Users has a favorite/required format to store information  SQL Relational Database, No-SQL, Excel Spreadsheet  XML, YAML, JSON or JSON-LD  Allows use in different ways – facilitates usage  Build a new data standard using ChAMP  Annotate an existing data standard  ChAMP should define the types of metadata and general organization of the information, not the format it is stored in (this is like MIAME [1]) Why a Platform (Toolkit)? [1] http://www.mged.org/Workgroups/MIAME/miame.html
  • 8.  Covers metadata for a chemical analysis methodology not raw analytical instrument data  Use existing technology/standards where-ever possible  Nothing is required – some things highly recommended  Can use all of specification, some parts, or only one piece  Useful for both method development and application  Platform scope should be as wide as possible  What information is most important?  How do we get community involvement/buy-in? First Thoughts
  • 9.  Description of important CA metadata  Taxonomy of CA metadata  Ontology of chemical analysis terms  Broad terms initially  Development of technique specific terms/concepts later  Controlled vocabularies for specific metadata items  Definitions of required metadata (in context)  Naming and design rules Pieces of the Puzzle
  • 10.  Ontologies  Chemical Methods Ontology (CMO) [2]  SemanticScience CHEMINF Ontology [3]  Chemical Entities of Biological Interest (ChEBI) [4]  Basic Formal Ontology [5]  Units of Measure Ontology [6] Existing Resources [2] http://www.rsc.org/ontologies/CMO/ [3] https://code.google.com/p/semanticscience/ [4] http://www.ebi.ac.uk/chebi/ [5] http://ifomis.uni-saarland.de/bfo/ [6] https://code.google.com/p/unit-ontology/
  • 11.  Controlled Vocabularies/Taxonomies  MESH [7]  LCSH [8]  CAS Subject Headings [9]  IUPAC Orange Book [10]  IUPAC Gold Book [11]  … do they address how to organize the metadata? Existing Resources [7] http://www.ncbi.nlm.nih.gov/mesh [8] http://id.loc.gov/authorities/subjects.html [9] http://cas.org [10] http://iupac.org/publications/analytical_compendium [11] http://goldbook.iupac.org/
  • 12.  Other  JCAMP-DX [12]  Analytical Information Markup Language (AnIML) [3]  Units Markup Language (UnitsML) [14]  NASA Quantities, Units, Dimensions and Data Types [15]  Electronic Laboratory Notebook Manifest (elnItemManifest) [16] Existing Resources [12] JCAMP-DX – http://www.jcamp-dx.org/ [13] AnIML – http://animl.sourceforge.net/ [14] UnitsML – http://unitsml.nist.gov/ [15] QUDT– http://qudt.org/ [16] elnItemManifest –http://www.jcheminf.com/content/5/1/52
  • 13. What are the Most Important Metadata?  Depends on who you talk to…  Platform should describe (as completely as possible) the types of metadata important in analysis…  … but leave the description of what’s important to the users  Standards for different industries, with different requirements, could be developed based on the platform
  • 14.  Minimal Information of A Microarray Experiment (MIAME)  http://fged.org/projects/miame/  Standards for Reporting Enzymology Data (STRENDA)  http://strenda.org/  Minimum Information for Biological and Biomedical Investigations (MIBBI)  http://www.biosharing.org/standards  Minimum Information required for a Glycomic Experiment (MIRAGE)  http://www.beilstein-institut.de/en/projects/mirage Minimal Amount of Information…
  • 15.  MIAChA (my-ache-a?)  Can the community agree on a minimum set of metadata items needed to annotate an analysis?  Must be for a more specific area of analysis  MIASA – Spectrochemical Analysis  MIACA – Chromatographic Analysis  MIAEA – Electrochemical Analysis  MIATA – Thermal Analysis Minimum Information About a Chemical Analysis?
  • 16.  Description  Infrastructure  SamplePrep  Analyte(s)  Sample(s)  Instrument(s)  Quality  Material(s)*  Concept(s)* Categories of Metadata Although the metadata is organized under these main areas implementers are free use only what they need and organize the metadata they need in any way. Reminder: ChAMP is focused on metadata about a chemical analysis, not about the instrument data that is generated when doing a chemical analysis (although they are of course related). * Still in development as of 3/10/15
  • 17.  title: the descriptive title of the method (string)  creator: who is the primary author responsible for this method (string) (ORCID or name)  description: textual description of the method (string)  analytical focus: what is the main reason for development of the method? (string) (e.g. improvement of the detection limit)  application area: broad area where the method will be most useful/used (string/enum) (e.g. 'pharmaceutical', 'environmental', 'petrochemical',...)  analysis type: what is the type of analysis done in the method (string/enum) (e.g. either 'quantitative', 'qualitative', 'property’)  analysis format: what is the format of the analysis (string/enum) (e.g. 'wet chemical', 'instrumental', 'sensor', 'remote')  analysis usage: in what context is the method to be used – general or specific (string/enum) (e.g. 'clinical trial', 'QC', 'QA', 'general')  analysis locale: the environment that the method has been developed for (string/enum) (e.g. 'laboratory', 'field', 'industrial plant', 'atmosphere’)  citation: literature citation (string) The ‘Description’ Category
  • 18.  contact: a specific individual that can be contacted about the analysis (string)  person: an individual that has participated in part in the development/production/publication of the chemical analysis (string)  organization: a company/institution/organization that was part of the development/production/publication of the chemical analysis (string)  funding agency: a public or private group that was a source of funding relative to the chemical analysis (string)  role: the part that a contact plays in the development/production/publication of the chemical analysis (string/enum)  address: physical address identifying the location of a contact (string)  phone: telephone number for communicating with a contact (string)  email: electronic mailing address for communicating with a contact (string)  location: a place where one or more activities was performed in the development/production/publication (e.g. building/lab) of the chemical analysis (string) The ‘Infrastructure’ Category
  • 19.  sample name: the name given to a sample (string)  subsample id: the unique identifier(s) of a subsample(s) (string)  subsample amount: the mass/volume of a subsample(s) processed for analysis (float/decimal)  subsample unit: the unit of the quantity of a subsample amount (string)  procedure: a textual description of the procedural steps used to convert the raw sample into a sample ready for analysis (string) -- OR -- step(s): each procedural step separately recorded with some indication of the order the steps were taken (string) (e.g. 1-10, A thru M)  storage conditions: how/where a sample is stored after laboratory processing, prior to analysis  chain of custody: whether a chain-of-custody was maintained and/or the chain of custody record  interferences: information about interference(s) that can be an issue in the sample preparation  safety: any safety issues relative the sample preparation (string)  waste: information about waste generated from the preparation procedure (string)  keywords: any important terms that characterize the sample preparation process (string)  reference: a formatted citation to a published version of the procedure used (string) The ‘SamplePrep’ Category
  • 20.  substance: a discrete chemical species identified by its InChI key/string (string)  substance class: named group of chemical substances identified as a specific class by structure, use, size, or action determined in chemical analysis procedures (string) (e.g. PCB's, amino acids, PAH's, pharmaceuticals, heavy metals, enzymes, etc.)  functional group: chemical test for an organic functional group (string)  biological property: a property specific to a biological process (string) (e.g. biological activity, QSAR)  chemical property: any property to due with a chemical reaction (string) (e.g. heat of combustion, enthalpy of formation, toxicity, rate of reaction, etc.)  physical property: measurement of a bulk (material) property, or characteristic substance property (string) (e.g. solubility, RI, electrical conductivity, etc.)  analyzed form: a descriptive term to indicate the state of the analyte as it was measured (oxidation state should be indicated in the InChI) (string) (e.g. dissolved, labile, total, volatile, extractable, free, residual, etc.) The ‘Analyte’ Category
  • 21.  identifier: the unique identifier of the sample (string)  amount: the mass or volume of the sample received or collected (float/decimal)  amount unit: the unit of the quantity of the sample amount (string/enum/vocab)  aggregation: if the sample was obtained by collecting it at multiple locations and combining then it should be described here (string)  matrix: description of the type of sample material (from a controlled vocabulary) (string)  physical state: the phase of the sample (e.g. solid, liquid, gas, slurry, etc.) (enum)  homogeneity: the homogeneity of the sample at collection (e.g. homogeneous, heterogeneous, emulsion) (enum)  field stabilization: a description of the any processes used to stabilize the sample in the field  field additives: list of substances added to the sample to stabilize the concentration of the analyte(s) to be determined (string)  storage container: container that the collected is stored/placed in for transport/storage (include material and container type)  storage conditions: how/where the sample is stored after collection, prior to lab processing and/or analysis The ‘Sample’ Category (1/2)
  • 22.  sampling event: was the sample collected as part of a specific trip/exploration/voyage? (string)  sampling location: a description of or GPS coordinates for where the sample was obtained (string)  sampling depth: the depth below sea level the sample was collected (string)  sampling depth unit: the unit for the sampling depth (string/enum/vocab)  sampling altitude: the altitude above sea level the sample was collected (string)  sampling altitude unit: the unit for the sampling altitude (string/enum/vocab)  sampling conditions: what were the environmental conditions (weather) where the sample was collected (string)  sampling protocol: how the sample was collected (string)  sampling equipment: the apparatus used to collect the sample (string) The ‘Sample’ Category (2/2)
  • 23.  instrument: the general type of instrument being used to the analysis (vocabulary)  apparatus: non-instrumental equipment used to do an analysis (string) (e.g. 50 mL burette, sintered glass crucible, etc.)  manufacturer: the name of the manufacturer of the instrument being used (string)  model number: the manufacturers model number used to identify the instrument (string)  serial number: the serial number of the instrument (string)  software name: name of the software used to run the instrument (string)  software version: version of the software used to run the instrument (string)  operating system: the operating system used to run the instrument software (string)  accessories: a list of any accessories installed onto the main instrument (string) (e.g. autosampler, fraction collector, etc.)  configuration: a textual description of the (physical) configuration of the instrument, used to highlight any unique/interesting aspects of the system (string)  settings: A textual list of the values used for important instrumental parameters (string) The ‘Technique’ Category
  • 24.  Metrics  Coefficient of Determination (R2)  Confidence Interval  Detection Limit  Limit of Quantitation  Chemometrics  F-test  Paired t-test  One-way ANOVA  Non-parametric Test  Validation  Quality Control (QC)  Statistical Process Control  SRM/CRM Analysis  Sample Spike Recovery  Example Data  Chromatogram  Peak Table  Spectrum  Calibration Curve The ‘Quality’ Category
  • 25.  An ontology to represent the concepts in the discipline of chemical analysis AND the metadata and data structures important to the area  Borrows heavily from  Chemical Methods Ontology  Chemical Information Ontology  Chemical Entities of Biological Interest Ontology  Basic Formal Ontology  Unit of Measure Ontology Chemical Analysis Ontology
  • 29.  Summary information for a journal article  Implementing ChAMP in XML  ChAMP XML Schema  Journal Article Metadata Specification Schema  Instance file (XML file for one journal article) Example Application
  • 33.  Publish version 1 of platform (with best practices)  General Concept Vocabulary for Chemical Analysis  Concept Vocabularies for Specific Techniques  Repurpose any existing vocabularies (with permission)  Convert/integrate IUPAC ‘terminology’ publications  Provide example documents in different formats  Additional example applications  Partner with groups in different areas Future Developments
  • 34. Conclusion  The ‘platform’ approach will make it easier for scientists to  Develop new standards for representing chemical analysis information  Integrate semantic annotation into exiting standards  It will enhance basic searching (through standardization and vocabularies)  It will allow semantic searching  It will provide efficient annotation of large amounts of curated data that is not from traditional publishing  Fits with the mission of the Research Data Alliance [16] [16] http://rd-alliance.org
  • 35.  schalk@unf.edu  Phone: 904-620-1938  Skype: stuartchalk  LinkedIn/Slidehare: https://www.linkedin.com/in/stuchalk  ORCID: http://orcid.org/0000-0002-0703-7776  ResearcherID: http://www.researcherid.com/rid/D-8577-2013 Questions?