1 / 15

eagle- i and ISF: a Brief History

eagle- i and ISF: a Brief History. 2009: eagle- i ontology (ERO) development begins 2011: the ISF is seeded with the complete eagle- i ontology and extended 2011-present : ERO and ISF ontologies diverge as they are independently developed

ferrol
Download Presentation

eagle- i and ISF: a Brief History

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  1. eagle-i and ISF: a Brief History • 2009: eagle-i ontology (ERO) development begins • 2011: the ISF is seeded with the complete eagle-i ontology and extended • 2011-present: ERO and ISF ontologies diverge as they are independently developed • original ERO content removed/changed in ISF, new content added to ERO, etc • Fall 2013: refactoring to harmonize diffs and allow automated generation of ERO from ISF

  2. Refactoring Goals • Harmonize diffs between eagle-icontent covered in ERO and ISF • Refactor the file modularization of ISF (from topic-based to source based approach, for easier updating) • Implement automated pipeline for generation of ERO core ontology from ISF content • Future development of core content in ISF

  3. Refactoring Workstream 1: Core Content • Identify Diffs: the master-diff script lists all axioms from ERO import chain that are different/missing in ISF • Trim MIREOTed axioms: leave only coreterm axioms (ero/isf/vivo) this curation workstream • Classifycore diffs and Resolve: via manual or automated approaches • ERO-Deprecated Terms: ERO contains deprecated terms it originally donated to ISF • ISF-Deprecated Axioms:  ISF has deprecated terms/axioms it originally imported from ERO • New ERO Axioms:ERO has created new terms/axioms not in the ISF • Inconsistent IRIs: the same concepts are represented by different terms/modeling in ERO vs ISF

  4. Refactoring Workstream 1: Core Content • Identify Diffs: the master-diff script lists all axioms from ERO import chain that are different/missing in ISF • Trim MIREOTed axioms: leave only coreterm axioms (ero/isf/vivo) this curation workstream • Classify core diffs and Resolve: via manual or automated approaches • ERO-Deprecated Terms: maintain terms in a separate file outside of ISF import chain (ei-deprecated.owl) • ISF-Deprecated Axioms: move axioms into a separate file outside of the ISF import chain (ei_local.owl) • New ERO Axioms: add axioms to ISF in separate file in the ISF import chain (isf_temp.owl), or (ei_local.owl) • Inconsistent IRIs: IRI mapping and merging is required to resolve IRI differences

  5. Refactoring Files for Core Content(Workstream 1) • ei_deprecated.owl- will hold terms that were deprecated in ERO. Will not be in ISF import chain. • isf_temp.owl– will hold axioms new to ERO that can be added to ISF. Will be read into the ISF import chain. • ei_local.owl- will hold axioms that belong only in ERO. Will not be part of the ISF import chain. • ero.owl– will be updated to align with ISF, and be deprecated for further development once first auto-generated version is made from ISF content. * no ISF files will be harmed in the curating of this ontology

  6. Refactoring Workstream2: MIREOTed Content • Goals: • Resolve any diffs in axioms related to MIREOTed terms • Move MIREOTed content into source-specific files to facilitate automated updates • MIREOTed content in ISF currently mixed in same owl files as core (ero/isf/vivo) content. The segregation of content in these files based on topic/domain (source folder) • Preferred modularization strategy is to segregate MIREOTed content by source ontology (as is currently done in eagle-I, e.g. obi_imports.owl, go_imports.owl)

  7. ei ISF

  8. Workstream 2: MIREOTed Content • ERO imports files will be copied/renamed into ‘mireots’ folder of ISF SVN (e.g. go_mireot.owl) • The mireot-refactorscript will read axioms in go_mireot.owl and look for these axioms in ISF files • axioms found in ISF files will remain in go_mireot.owl • axioms absent in ISF files will be triaged in go_mireot-new.owl • Curators manually review mireot-new axioms and move to go_mireot.owlas approved. • Any axioms remaining in source ISF files that declare GO terms will be reviewed and moved to go_mireot.owlif appropriate.

  9. Workstream 2 Outcomes • The ISF ‘source’ files should not contain any declarations of MIREOTed terms (but these classes can be referenced in axioms on other classes). • The ‘mireot’ folder files will contain all MIREOTed terms separated into source-specific files (go_mireot.owl, obi_mireot.owl)

  10. Workstream 3: ERO view from ISF • Once all diffs resolved as outlined above, all content needed to generate ero.owl should exist in the ISF import chain and accessory local ei files: • ei_deprecated.owl • isf_temp.owl • ei_local.owl • Tools/scripts we will use here not yet determined (Ontodog, OWL-tools, custom script) • Will also need to define approach for evaluating new ERO ontology for completeness, consistency, and its support of eagle-i applications

  11. Documentation • Issues and progress tracked in ERO google code, tagged with ‘ISFmigration’: • http://code.google.com/p/eagle-i/issues • Specific changes are to be tracked in an xls spreadsheet shared by curators

  12. Refactoring Workflow • Identify Diffs: the ‘master-diff’ script lists all axioms from ERO import chain that are different/missing in ISF • Separate mireoted term diffs from core term diffs (ero/isf/vivo) for different curation workstreams • Workstream 1: Classify core diffs and resolve via manual or automated approaches • ERO-Deprecated Terms: maintain terms in a separate file outside of ISF import chain (ei-deprecated.owl) • New ERO Axioms:add axioms to ISF in separate file in the ISF import chain (isf_temp.owl) • ISF-Deprecated Axioms:move axioms into a separate file outside of the ISF import chain (ei_local.owl) • Different IRIs for same concepts: IRI mapping and merging is required to resolve IRI differences

  13. Refactoring Workflow • Identify Diffs: the master-diff script lists all axioms from ERO import chain that are different/missing in ISF • Separate mireoted term axioms from core term axioms (ero/isf/vivo) for different curation workstreams • Workstream 1: Classify core diffs and resolve via manual or automated approaches • ERO-Deprecated Terms: ERO contains deprecated terms it originally donated to ISF • New ERO Axioms:ERO has created new terms/axioms not in the ISF • ISF-Deprecated Axioms:  ISF has deprecated terms it originally imported from ERO • Different IRIs for same concepts: the same concepts are represented by different terms/modeling in ERO vs ISF

  14. Refactoring Workflow • Identify Diffs: the ‘master-diff’ script lists all axioms from ERO import chain that are different/missing in ISF • Separate mireoted term diffs from core term diffs (ero/isf/vivo) for different curation workstreams • Workstream 1: Classify core diffs and resolve via manual or automated approaches • ERO-Deprecated Terms: maintain terms in a separate file outside of ISF import chain (ei-deprecated.owl) • New ERO Axioms:add axioms to ISF in separate file in the ISF import chain (isf_temp.owl) • ISF-Deprecated Axioms:move axioms into a separate file outside of the ISF import chain (ei_local.owl) • Different IRIs for same concepts: IRI mapping and merging is required to resolve IRI differences

More Related