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Ontomaton icbo2013-alternative order-t_wv3
 

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Ontomaton: NCBO BioPortal Ontology lookups in Google Spreadsheets produced by ISATeam at University of Oxford e-Research Centre (Eamonn Maguire, Alejandra Gonzalez-Beltran, Philippe Rocca-Serra and ...

Ontomaton: NCBO BioPortal Ontology lookups in Google Spreadsheets produced by ISATeam at University of Oxford e-Research Centre (Eamonn Maguire, Alejandra Gonzalez-Beltran, Philippe Rocca-Serra and Susanna Sansone) and NCBO (Trish Whetzel).

The work was presented during ICBO 2013 in Montreal by Trish Whetzel (Thanks Trish!)

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  • Thank the Organizing committee for selecting our manuscript for this highlight session, which was published last February as an application note in Bioinformatics, an OUP journal, as collaboration between NCBO Bioportal and ISA commons.
  • We could have a diagram for the context, showing the different teams, geographically distributed and sending spreadsheets back and forward only flattened hierarchies available as (long) drop-down lists)
  • He’s happy because he’s part of a big family of others tools (This is an overview of the resources developed by the ISA team to support management of experimental data. One the most salient feature of the toolkit is ISAcreator) and it inherits from ISAcreator some very nice functionalities such as the ontology lookup (Go to Slide 4) and tagging ( Go to Slide 6), courtesy of bioportal web services
  • ISAcreator made a splash a few years back for bringing together spreadsheet functionality and ontology lookup and tagging in one same standalone java application and has inspired a number of tools. Annotation restrictions, including Ontology selection and, within one resource, branch selection can be set via another tools: ISAconfigurator, which access the same ontology library as the ISAcreator. This has been made possible by the available for ontology services and web service programmatic access, which enabled third party applications to query hierarchies. A key feature, beyond the simple ability to perform lookups and searches, consists in allowing class metadata access, which provides further support for accurate usage of the resource. Once a configuration has been defined, ISAcreator Editor can read it the spreadsheet will be aware of the terminology restrictions a set by the super user in charge of defining annotation requirements. In this screenshot, you can see the allowed values for reporting Flow cytometry instrument using OBI classes in an Flow Cytometry Assay as defined in ISAconfigurator. Note the Metadata pulled from OBI and readily available for people to check the term they select is correct.
  • Another service provided by NCBO Bioportal powers the term tagging function in ISAcreator. Ranked hits are presented to the users, again, alongside class metadata to facilitate disambiguation and decision.
  • We could have a diagram for the context, showing the different teams, geographically distributed and sending spreadsheets back and forward only flattened hierarchies available as (long) drop-down lists)
  • He’s happy because he’s part of a big family of others tools (This is an overview of the resources developed by the ISA team to support management of experimental data. One the most salient feature of the toolkit is ISAcreator) and it inherits from ISAcreator some very nice functionalities such as the ontology lookup (Go to Slide 4) and tagging ( Go to Slide 6), courtesy of bioportal web services
  • Here is the problem: a multicentric study with participating centres across continents: the traveling jetlagged spreadsheet (never in synch)! [Then read the bullet points of the box. ]
  • Let’s dig more into OntoMaton and see how to use it!
  • And of course, the very nice thing of fusing with Google Document is that we have revision history always available! And collaborative editing !
  • You are all set to begin using the tool: Simply go to the Ontomaton Menu and choose from the various options, we’ll start with ‘Search function’, which brings in the widget windows, which can be moved around by clicking and maintaining the ‘move’ label at the top left hand corner of the box. Enter a string in the search box, hit search. A progress indicator will run, indicating that service is being invoked and waiting for results to be returned. Those are then display as tree list organized by resources which contain a hit. There are 2 buttons associated with each entry: one for selecting the value, one for obtaining more information. This last button pulls class metadata from NCBO bioportal service which are displayed in the sliding pane in the bottom right hand corner of the screen
  • Finally, invoking Biportal tagging service is just as simple, Go to the Ontomaton menu, hit ‘tag’ and follow a very similar procedure. If no restriction has been imposed, the string found in the cell or cell selection will be passed to the service and all hits will be presented in the widget window.
  • What powers it? Well a REST service call to NCBO bioportal services performed by Google scripts , some cool javascripting and smart rendering
  • But first thing first, OntoMaton needs to be introduced to its google doc. Installing is straightforward. It has to be done for each newly created google spreadsheet, for it to be available or one has to create a google template. To install from a naïve google spreadsheet, go to the ‘Tools’ menu, then go to the ‘Script Gallery’, search on ‘ontology’ or ‘ ontomaton ’ , there is only one hit. Click Install, done, wait a bit or hit the refresh button, Ontomaton Menu should now appear in the Menu bar as shown in those screenshots
  • Once installed, the things to know is that various settings can be tweaked to alter OntoMaton ’ s behaviour. To do so, go to the Menu Ontomaton, then Setting. Ontomaton extension offers several working options: First, one can choose from 2 options defining how purls should be saved and displayed: either by creating an hyperlink in the cell, or split the information over 2 fields (to mimick ISA-Tab syntax) Another key functionality available from the setting pane, is that ability to specify for any given field in the annotation spreadsheets, which resource or resources should be used. This serves the purpose of limiting the search space. For instance, a field ‘organism’ may restricted to only search the Amphibian Anatomy Ontology or NCBI Taxonomy. (second image) As you can see, a new worksheet is automatically created that holds on the ‘restrictions’ parameters, which feed in the Ontomaton lookup and tagging functions.(third image)
  • Let ’ s see now how OntoMaton can help and go over 3 use cases/
  • The first application is in the context of ISA commons framework. ISA configurations are exported as Excel files, holding all restrictions and terminology settings. The excel document is then uploaded as Gdoc to create a GoogleTemplates which can be invoked and used for tracking experimental metadata, essentially acting as a collaborative lims.
  • The first application is in the context of ISA commons framework. ISA configurations are exported as Excel files, holding all restrictions and terminology settings. The excel document is then uploaded as Gdoc to create a GoogleTemplates which can be invoked and used for tracking experimental metadata, essentially acting as a collaborative lims.
  • The second application was again in ISA context but for an entirely different purpose. It was taken advantage of for performing mappings from ISA syntactic element to semantic frameworks, mappings which can then be used to convert ISA-Tab documents into OWL thanks to the ISA2OWL converter. The main benefit here is the ability to perform the mapping collaboratively while tracking all the changes automatically.
  • The last application is the creation of Quick Term Templates (described during the first ICBO meeting) , i.e. as ontology design patterns based class addition templates (things that have exploited by OBI using excel or tools such as Populous). Now, this can be done (the mapping at least) using gdoc , making it easier to collaboratively review / edit the defined classes once a pattern has been identified. (TODO screenshot is missing) So the take home message is really, ontomaton is developed by ISA team and while the initial use was meant to provide support for ISA-Tab syntax in a collaborative context, it can be used in any spreadsheet layout for any purpose which need terminology support for annotation tasks, irrespective of ISA.
  • . Who’s using Ontomaton: Several groups coming from the ISAcommons community have been benefitting from the functionality: Bioplatforms Australia for managing distributed soil metagenomics projects, NBIC in the netherland is very keen to use Ontomaton for the potential it has in helping the creation of nanopublications. TODO: Add CaNanoTab logo  
  • Last slide with all the necessary information: check out Github site, there is a video tutorial on youtube and and if you to work with us to extend functionality, get in touch. This last point leads us to future plans and collaborations. If anyone is interesting to work with us, get in touch on github
  • Here is the problem: a multicentric study with participating centres across continents: the traveling jetlagged spreadsheet (never in synch)! [Then read the bullet points of the box. ]
  • What powers it? Well a REST service call to NCBO bioportal services performed by Google scripts , some cool javascripting and smart rendering
  • We could have a diagram for the context, showing the different teams, geographically distributed and sending spreadsheets back and forward only flattened hierarchies available as (long) drop-down lists)
  • The origin of ontomaton can be traced to ISAcreator and its functionalities. So a star wars inspired dialogue between ISAcreator and Ontomaton would go like this : ISA creator would say “I am your father” but no drama here, Ontomaton is quite pleased with that!  

Ontomaton icbo2013-alternative order-t_wv3 Ontomaton icbo2013-alternative order-t_wv3 Presentation Transcript

  • OntoMaton: a BioPortal-powered ontology widget for Google Spreadsheets. Bioinformatics. 2013 Feb 15;29(4):525-7. doi: 10.1093/bioinformatics/bts718 ICBO 2013, Paper Highlight, Presented by Trish Whetzel Eamonn Maguire, Alejandra González-Beltrán, Patricia L. Whetzel, Susanna-Assunta Sansone and Philippe Rocca-Serra
  • Motivations • Geographically distributed collaborators • Spreadsheets used to collect data • Potential for conflicting versions • Need to maintain provenance • Need to provide ontology look-ups • Need for collaborative editing
  • ISAcreator: Ontology Lookup and Term Selection
  • ISAcreator: Ontology markup via NCBO Annotator Curation of datasets imported or converted from other formats
  • Motivations • Geographically distributed collaborators ü Spreadsheets used to collect data • Potential for conflicting versions • Need to maintain provenance ü Need to provide ontology look-ups • Need for collaborative editing
  • a BioPortal-powered ontology widget for Google Spreadsheets
  • OntoMaton: Leverages Google Spreadsheets Collaborative editingProvenance trackingVersion control
  • OntoMaton: Searching
  • OntoMaton: Searching
  • OntoMaton:Tagging
  • h"p://rest.bioontology.org Ontology   Services • Search • Traverse • Comment • Download Widgets • Tree-­‐view • Auto-­‐complete • Graph-­‐view AnnotaCon Data  Access Mapping   Services • Create • Upload • Download Term  recogniCon Search  “data”   annotated  with  a     given  term NCBO Web services
  • h"p://rest.bioontology.org Ontology   Services • Search • Traverse • Comment • Download Widgets • Tree-­‐view • Auto-­‐complete • Graph-­‐view AnnotaCon Data  Access Mapping   Services • Create • Upload • Download Term  recogniCon Search  “data”   annotated  with  a     given  term NCBO Web services
  • h"p://rest.bioontology.org Ontology   Services • Search • Traverse • Comment • Download Widgets • Tree-­‐view • Auto-­‐complete • Graph-­‐view AnnotaCon Data  Access Mapping   Services • Create • Upload • Download Term  recogniCon Search  “data”   annotated  with  a     given  term NCBO Web services
  • OntoMaton: Installation
  • OntoMaton: Installation
  • OntoMaton: Installation
  • OntoMaton: Installation
  • OntoMaton: Installation
  • OntoMaton: Installation
  • OntoMaton: Settings
  • OntoMaton: Settings
  • OntoMaton: Settings
  • OntoMaton: Settings
  • OntoMaton: Settings
  • Applications
  • Application I: Collaborative ISA
  • Application II: Mapping
  • Application III: QTT pattern based ontology building / expansion
  • User Community
  • A  growing  ecosystem   of  over  30  public  and  internal  resources  using  the  ISA  metadata  tracking  framework   to  facilitate  standards-­‐compliant  collec@on,  cura@on,  management  and  reuse  of  inves@ga@ons  in  an   increasingly  diverse  set  of  life  science  domains. Towards  interoperable  bioscience  data Sansone  et  al,  2012 Nature  Gene@cs
  • Source Code & Documentation
  • https://github.com/ISA-tools/OntoMaton
  • OntoMaton: a BioPortal powered Ontology widget for Google Spreadsheets Maguire et al, 2013 Bioinformatics Thank you!