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NIF Workflows

NIF Workflows. Ashraf Memon. Data Registration Workflow. Applies to level 1. Feedback. NIF User. Jira. Enter the URL for review. Enter Descriptions + NIF Terms + Resource Type. Categorize These Resources. E mail. Curation. Curation. Search. Reference. Survey Monkey. | | | |.

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NIF Workflows

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  1. NIF Workflows Ashraf Memon

  2. Data Registration Workflow Applies to level 1 Feedback NIF User Jira Enter the URL for review Enter Descriptions + NIF Terms + Resource Type Categorize These Resources Email Curation Curation Search Reference Survey Monkey | | | | | | | | | | | | | | | | Curation Revisit Approved Declined Preliminary List Copy to NIF Web and Notify Curator Crawl, Create Indices and Notify Curator Upload to the Server Incorporate Curation Cronjob Cronjob NIF Web | | | | | | | | | | | | Indices NIF Registry Server Registry

  3. Ontology Registration Continues Process Bulk upload request of Terms Email NIF User Identify concepts, relationship and modules from wiki and emails Enter Terms in Neurolex Wiki Update Owl Files (Testing Environment) Curation Curation Neurolex Wiki (Production) | | | | Test and Feedback OWL file Program Register OWL with Neurolex Curation Release PURL Create a persistent link to archived version of NIFSTD Test in OntoQuest Test OWL with Bio-portal Register OWL with PURL Register OWL with OntoQuest OntoQuest Update project Wiki with release notes Register OWL with Bio-portal Project WIki Bio-Portal

  4. 2. Bulk Upload Request of Terms Feedback 1. Add/Edit NeuroLex Terms/Categories 3. Identify Valid Contributions 4. Update NIFSTD (Testing) NIF Users RELEASE 5. Testing in OntoQuest NeuroLex Wiki 9. Update NIFSTD (Production) | | | | 6. Testing in BioPortal NIFSTD OWL Files 10. Update NeuroLex NeuroLex 11. Update OntoQuest 7. Keep Persistent Link to Older Versions || || OntoQuest 12. Update BioPortal NIFSTD OWL Files (Pointing to PURLs) 8. Update Project Wiki Release Notes BioPortal 13. Update TextPresso Bucket TextPresso

  5. This workflow includes the tasks mentioned in each of the rectangular boxes followed by a numbers. Each of the tasks are further explained below • 1. Add/Update terms (Categories): The main interface between NIF vocabularies (extracted from NIFSTD owl files) is the NeuroLex wiki. We expect the NIF users to contribute/edit the NIF terms through the NeuroLex. NeuroLex wiki is the main entry point for NIF users to access the NIF vocabularies. This step involves various NIF user groups who are interested to contribute to NIF or use the standard NIF vocabularies for their projects. • 2. Bulk Upload of Terms: Depending on the nature (i.e, new subtree for an existing NIF term, list of brand new terms for a specific NIF module etc.) and number of terms, we can have bulk upload of those terms (spread sheet etc.) from our collaborative group. These requests can be made through wiki or direct e-mail communication. (colleboration with Maryann and Fahim) • 3. Identify Valid Contribution: This step involves identifying the contributions in the NeuroLex wiki that are valid for NIF STD ontology. Therefore, not all contributions can be implemented in NIFSTD ontlogy for the sake of univocality, consistentency and relevance to Neuroscience. Especially for new terms we need to make sure that the term is actually a new one and not a synonym or duplicate of existing terms (collaboration with Maryann Martone) • 4. Update NIFSTD (testing): This step involves updating the NIFSTD OWL files in testing environment based on the updates/addition of contents from previous steps. ( Collaboration with Fahim Imam) • 5. Testing in OntoQuest: After significant update in the owl files (Every 1-1.5 months), the NIFTD goes to OntoQuest testing for feedback. (Colleboration with Xufei and Amarnath, OntoQuest group) • 6. Testing in BioPortal: The NIFSTD owl files are tested in BioPortal Staging for feedback. (Colleboration with Trish, BioPortal Group) • 7. Keep persitent links to older versions: After positive feed back from 5 and 6, we archive the links to the old owl files and post the links to the Project wiki (Fahim) • 8. Update project wiki release notes: Before releasing the production version, add a new release note for the new version. (Fahim, Maryann, Sarah, Stephen) • 9. Update NIFSTD (Production): This step involves updating the NIFSTD owl files in the production server that pointed by PURL links • 10. Update NeuroLex Wiki: Each release will be followed by an Update in NeuroLex which will reflect the implemented changes /addition of the NIF contents in the preveious iteration. (Colleboration with Stephen) • 13. Update TextPresso Bucket: Textpresso group should be updated after each new release of NIFSTD (Colleboration with Arun)

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