Action Items
From Program on Ontologies of Neural Structures
Contents |
NRTF Action items:
- For Kobe demonstration:
- Create a set of entity lists that NRTF needs to complete this demo
- Contribute definitions that the group already has in difference resources
- Create specific queries that might be used for this demonstration, also generate additional queries in areas outside of hippocampus to ensure what we build isn’t too focused on one area
- Have electrophysiologists review our interfaces (Neurolex, Giorgio’s, and Paul’s) to see if it is possible for them to describe electrophysiology characteristics. Examine OWL for limitations
- Review relevant ontologies in a systematic manner
- Review current terms in Giorgio’s and NeuroLex interface to see how an ontologist would structure them. Examine property list and determine how it can be divided into properties and values and how it relates to ontologies
- Look at definitions in sense lab (Giorgio) and put them into GO
- Compile existing and missing textual definitions of locations for the entorhinal-hippocampal complex (notably, layers) from Menno’s interface and determine how to sync with NeuroLex in the future (Menno, send to Jyl & Giorgio for distribution to NeuroLex and other PONs)
- Convergence on a set of core properties that are likely to be commonly considered “necessary and sufficient” to describe a cell e.g. a few use cases suggested 3-4 descriptors would do, likely including location and/or shape of some combination of soma, dendrites, and axon, as well as the neurotransmitter, possibly the cell marker, and firing pattern was good to have but did necessarily seem to be a defining characteristic for these use cases.
- Annotation of neurons:
- Menno: an entorhinal and a presubicular neuron
- Sean: S1 (non-barrel) Martinotti cell and S1 (non-barrel) nested basket cell
- Gordon: two (potentially more) undecided cells
- Complete annotation of 8 more cells from remaining NRTF members (NRTF members) [mid-April]
- People must also define properties if they don’t already exist
- Ensure properties we define and create is handed over to PATO
- Work with the cell graph and convert into OWL (David OS)
- Complete the Excel template with relations, values, property structure, and one plausible-looking example and circulate to Jyl, Menno, Sean, Gordon, and David OS (Giorgio)
- Map relations and values to existing unique identifiers in NeuroLex or exisiting ontologies, and note the missing ones (David OS) [mid-February]
- Write up NRTF operating principles we agreed on and circulate to TF (Giorgio)
- Implement a working interface for use by task force members and test it with 14 above examples (Giorgio) [July]
- Ensure interoperability of wiki, spreadsheet, and curator interface with model formalism, access to current ontology terms, definitions, and synonyms (Giorgio, Stephen, RDTF) [July]
SLTF Action Items:
- For Kobe demonstration:
- Create a set of entity lists that SLTF needs to complete this demo
- Contribute definitions that the group already has in difference resources
- Create specific queries that might be used for this demonstration, also generate additional queries in areas outside of hippocampus to ensure what we build isn’t too focused on one area
- List of consensus structures for mammalian brains (Laszlo, Maryann and Doug)
- March 31st: Review Doug’s Rosetta Stone structures and proposed hierarchy
- Identify which ones are consensus between rodent and primate
- Add the appropriate structure to the Neurolex
- WHS structures delineated with consensus structures (Laszlo)
- Protocol one day meeting ~April (Laszlo, Doug, Maryann, Seth, Jyl)
- Subset of x number of structures ready by Kobe
- Finish structure delineations within a year
- Add all rodent brain structures in BAMS to Neurolex Wiki (Stephen and Mihail)
- For Allen Atlas Brain Structures, link to the Scalable Brain Atlas structures (Rembrandt and Stephen)
- Add each parcellation scheme to the Neurolex (can some major ones be added by Kobe?) (Stephen, Alan, Maryann, Doug, David VE, Maryann, Jyl)
- Determine naming protocol (Alan)
- Properties of each parcellation need to be defined (e.g. defining criteria) (perhaps Mihail, Doug, David VE, Maryann)
- Ensure synonyms and equivalencies are recognized (BAMS and BrainInfo have much of this information)
- Tie different nomenclature parcellations to the NeuroLex consensus structures and preferably to an atlas. Get some started before Kobe, a year and beyond (BAMS, BrainInfo, David VE, Menno)
- Recommend best practices for new brain parcellations (begin after Kobe)
- Protocol
- Best practices
- Define all properties associated with Brain Regions in NeuroLex
- Ensure that connectivity property can be expressed in terms of neuron to neuron connectivity property from NRTF
- Create OWL representation of BAMS (Alan and Mihail)
- Investigate Scalable Brain Atlas (SBA) copyright issues with (Paxinos) (INCF, Gully)
- Investigate legal issues of getting Swanson into SBA (Mihail)
Issues for RDTF:
- Help determine the workflow and coordination among resources: What should go where? Content will be exposed through Neurolex Wiki, but we have multiple resources with representations that should be populated.
- NeuroLex
- BAMS
- FMA
- Brain Info
- etc.
- Who will define the higher level “data types”, e.g., populations of cells, that will be necessary for some of the cross scale anatomy?
- Cell component from NIF is being submitted to GO (Chris Mungall is submitting them and NIF ID is becoming secondary ID). NIF has to maintain a mapping.
- Recommendation: GO should maintain them as secondary IDs. A process needs to be put into place to handle this.
- We will need multiple models from RDTH for how to formalize:
- brain region (above)
- a cell
- a population of cells
- Owl file is standard, but set workflow for syncing to other infrastructure
- also develop recommendations for how others might extend this
- Outline set of properties so that inferences can be made across scales
- e.g. brain region X projects to brain region Y if principle neuron with soma or dendrites in brain region X contacts cell with part of cell in brain region Y
- Put the example cell created by Sean and Giorgio into OWL
- Split to work more with the other TFs with occasional sessions within the group
- Determine if meeting in Kobe for review of best practices for hierarchies
Infrastructure:
- Create nomenclature pages
- Create disambiguation pages (so people can see synonyms while entering) e.g. NeuroLex wiki: high priority, but easy to do via curation (do you mean this, this, this, or this)
- Define wiki and OBO foundry ontology process for interaction and what needs to be embedded in NeuroLex. How to define things in terms of the other ontologies and to import mechanisms and just the pieces we need. Define some processes and tools. (Alan, David OS, Maryann, Stephen), first pass cell component with GO, should be a process by Kobe (and hopefully some level of automation). Alan and David OS will start discussing this first soon
- Determine Scalable brain atlas (SBA) issues with Paxinos copyright (Rolf, Rembrandt, INCF and Gully).
- NeuroLex images of structures need to be linked to the images
- mouse: ABA images via SBA
- macaque and human: via Webcarat and SBA (probably faster)
- rat and mouse hippocampus: Menno
- look into Google 3D plug-in and 3D PDF (Stephen)
- Recommend best practices for a common model to be used for the major atlas hierarchies (how to join together anatomical parts; this is how it should be expressed, OWL or OBO and use certain sets of relations, etc.). May not have this in place by Kobe, but could have a start and then work while there
- Services for accessing ontology
- 3 months to start pushing data between NeuroLex and Owl (BAMS and FMA)
