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Major Release and Progress

NIFSTD Release 2.9.6

  • Version: NIFSTD 2.9.6, Date: July 18, 2013
  • PURL Location: http://purl.org/nif/ontology/nif.owl
  • Inclusion of UBERON as a new NIFSTD module
    • The equivalency statements between NIF-Gross Anatomy and UBERON classes are kept in a bridge file
      • Bridge location: http://purl.org/nif/ontology/BiomaterialEntities/NIF-UBERON-Bridge.owl
      • This is the NIF version of UBERON-NIF-GrossAnatomy-Bridge. This is essentially a modified version of the UBERON-NIF Bridge file located at:  <http://goo.gl/ng4036>               
      •  The modifications include the following:
        • Added axioms to place UBERON's 'anatomical entity' and  'processual entity' under BFO independent_continuant and Occurant (not kept equivalent as BFO's 'processual_entity').
        • Replaced the PURL URIs for NIF-GrossAnatomy with the original NIF URIs within this bridge
        • Removed the underscores before the NIF class Identifiers and placed the deprecated UBERON classes under _retired_class.
  • Inclusion of a new version of NIF-GO-CC-Bridge
  • Inclusion of Eagle-I ontology as a new NIFSTD module
  • Inclusion of a new version of NIF-DOID-Bridge
    • Bridge location: http://ontology.neuinfo.org/NIF/Dysfunction/NIF-DOID-Bridge.owl
    • This bridge  assters mapping equivalencies between DOID and NIF-Dysfunction for 183 classes . The mapping is based on the exercise between NIF and DOID developers. 
      This mapping is effective for the current version of DOID. (July 17 version).
  • Replaced the old PURLS with the new ones for SO and NCBITaxonomy-Slim modules (Thanks to Trish for the detection). Fixed the dependency issues due to these changes.


NIFSTD Release 2.9

  • Version: NIFSTD 2.9, Date: December 10, 2012
  • PURL Location: http://purl.org/nif/ontology/nif.owl

  • Addition of NEMO Ontology as an import for NIF-Investigation module.
  • Addition of Cognitive Atlas Ontology (CogAt) as part of NIF-Investigation. 
    • Note: We have only imported the  'concept' classes from Cognitive Atlas and excluded the 'task' classes for now.
  • Added 'Neuroimaging' and 'Immunolabeling' as defined classes with corresponding roles.
  • Additional partonomy relations in NIF-Anatomy.
    • Fixed a number of reasoning issues with NIF-Anatomy module.  
  • Added Neuropathy, Giant axonal neuropathy etc. from Neurolex and some hierarchical changes in NIF-Dysfunction. 
    • Fixed the unresolved URI issue with DOID. Currently Imported the latest version of DOID.
  • Additional contributions from NeuroLex.
  • nif-backend.owl has been further simplified
    • The following modules are no longer needed: obo-foundry-core.owl which in turn called obo-foundry-core-full-import.owl.
    • This module now directly imports the following OWL modules only: BFO 1.1, RO, PATO, RO-BFO-Bridge, and Quality-BFO-Bridge   

NIFSTD Release 2.8

  • Version: NIFSTD 2.8, Date: May 12, 2012
  • PURL Location: http://purl.org/nif/ontology/nif.owl

  • OBO-OWL converted files: the new translation of the external ontologies are incorporated 
    • OBO-to-OWL converted modules in use: GO, PRO, DOID, SO, RO, and PATO.
  • Re-designed brain regions hierarchy in NIF-GrossAnatomy.owl
    • Significant enhancement of partonomy restrictions between brain regions as contributed in NeuroLex.
    • All parts of brain in NIFSTD are now asserted as 'Regional parts of brain'.
    • Inferred classification of 'specific regional part' of brain is still possible.
  • Resource hierarchy has been modified
    • Modified the hierarchy of 'Data set'. All the subclasses of 'Data set' are kept as 'Information content entity'. 
    • Modified the 'Semi structured knowledge' hierarchy. Currently it only includes Atlas, Bibliography, and Data set.  
  • Resolved reasoning issues with inconsistent classes.
  • Gene Ontology(GO) Biological Function is now a part of NIFSTD along with GO Cellular Component and GO Biological process.
  • Classes from externally maintained ontologies (GO, PRO, DOID etc.) in NIFSTD is now displayable in NeuroLex through OntoQuest web services.
    –Whenever the NIF Search system hits a “non-existent category” page for any NIFSTD class,  specific OnoQuest web service is called  to display the content of the class analogous to other pages.
    –The contents of these kinds will be maintained as ‘non-editable’ and will be displayed dynamically, reflecting whatever exist within the source ontologies.
    –Further works to be considered: NeuroLex users should be able to ‘append’ new contents on top of the non-editable content, e.g., definition, synonym,  asserting relational properties with other pages, just like any other NeuroLex page. An idea of  invoking a tracking system for these additions should also be considered.

 

NIFSTD Release 2.5

  • Simpler upper level hierarchy: This current version of NIFSTD only includes the following three classes as the most abstract ‘Thing’: entity (BFO), _limbo_class, _rertired_class, and _backend_entity
    • _backend_entity:  This class is the parent class of all the common 'backend' components necessary for each of the individual NIFSTD modules. These entities are from SKOS, Dublin Core Meta Data, Protege-DC, and 'extra' classes generated by OBO-to-OWL (oboInOwl) converted ontologies.
    • SO upper level classes are grouped under ‘Generically_dependent_continuent’ for now.
    • Individual NIFSTD modulesare now loadable without having to import the nif-backend.owl independently as before.
      • Loading all the modules together through the main, umbrella module (nif.owl) should not be disrupted due to this change.
      • This change would not affect the loading time either as loading all the modules together would be treated as including the nif_backend components just once.
  • The modules related to nif_backend.owl are simplified and kept as local i.e., the imports within the nif_backend.owl are all ‘direct’ from the local copies under a simple hierarchy of imports.
  • Inclusion of a slim version of NCBI Taxonomy organisms; English names are kept as alternative label.
    • A bridging module is maintained to set the mapping (equivalent) organisms between this slim of NCBI Taxonomy and those existed in NIF-Organism module before.
    • Defined classes: non-human primate and non-human vertebrate.
  • Bridging modules are enhanced to include more logical restrictions allowing previously defined classesto classify more neuron types.
    • More neurons have been updated with new restrictions which are inferred under previously defined neuron types.
  • Fixed the restrictions related to ‘roles’/ ‘has roles’/ ‘is bearer of’ in NIFSTD which had erroneous assertions from NeuroLex. Major inconsistencies are fixed.  
    • Nif.owl includes the modules that contain the saved inferred classification axioms.
  • Converted all the Core NIFSTD modules to the simpler, default RDF/XML OWL syntax as used in Protégé 4.X.
    • They can still be loaded in any previous versions of Protégé i.e., v3.X
    • This should allow us to eventually move towards utilizing OWL2 capabilities
  • Additional partomoy restrictions within NIF-GrossAnatomy.  Other bridging modules are improved to accommodate more defined concepts.
  • Protein Ontology(PRO) has been included as one of the imports for NIFSTD
    • There is a bridging module that asserts equivalencies between the classes from PRO and NIF-Molecule module. There should be more mapping equivalencies in the future.
  • Addition of Disease Ontology(DOID) as an import for NIFSTD  
  • New contents with enhanced annotations from NeuroLex contributions (Jan--Aug, 2011)
  • Classes from externally maintained ontologies (GO, PRO, DOID etc.) in NIFSTD will be displayed in NeuroLex through OntoQuest web services. The idea is as follows:
    • Whenever the NIF Search system hits a “non-existent category” page for any NIFSTD class, the OnoQuest web service will be called to display the content of the class analogous to other NeuroLex.
    • The contents of these kinds will be maintained as ‘non-editable’ and will be displayed dynamically, reflecting whatever exist within the source ontologies.
    • NeuroLex users will be able to ‘append’ new things on top of the non-editable content, e.g., definition, synonym, defining object properties, just like any other NeuroLex page. An idea of  invoking a tracking system for these additions will be considered soon.

NIFSTD Release 2.2

  • New bridging modules to include restrictions and defined classes to further classify various neuron types.
    • Neurons by soma locations in specific brain regions: Cerebellum cortex neuron, Cerebellum nucleus neuron.
    • More neurons have been updated with new restrictions which are inferred under previously defined neuron types.
    • Neurons that are the bearer of ‘Motor role of nerve cell’ are classified under ‘Motor neuron’
    • Neurons by molecular constituents:  Parvalbumin neuron, Calbindin neuron
    • Neurons by morphology: Spiny neuron. Other neurons with soma shapes are also there with necessary restrictions but was not defined (e.g., unlike Spiny neurons,  Pyramidal shape of a cell some does not  necessarily and sufficiently entail a pyramidal neuron)
  • Additional partomoy restrictions within NIF-Anatomy.  Other bridging modules are improved to accommodate more defined concepts.
    • Included parts of brain associated with the concept of ‘White matter’
    • Additional defined concepts: Basal Ganglia, Circumventricular organs under Gross-Anatomy module; Tracer, Anterograde tracer, Retrograde tracer, Transneuronal tracer under Molecule module
    • Inclusion of Differential gene expressions - Increased/Decreased expressions
  • COGPO ontologyhas been included as a new import module
    • Worked on Dr. Jessica Turner's version - added the numaric IDs for the CogPO classes (format is COGPO_XXXXX) and kept the class labels without any underscores following the standard naming conventions.
  • GO Cell component has been included as a new module
  • There is a bridging module between Human Disease Ontology (DOID)and NIF-Dysfunction that specifies the mapping equivalencies between the two ontologies
  • New contents with enhanced annotations from NeuroLex contributions from March till December 2010. 
  • Cleaned up the annotation properties in NIFSTD that were redundant  in multiple modules due to the modularization of original BIRNLex contents in the past.
  • OntoQuest Web Services for NIFSTD ontologies are listed with instruction in the following link (developed by Xufei Qian)

NIFSTD Release 1.8

  • Further modification of upper level NIFSTD classes under BFO.
    • Eliminated the distinction between snap:object and snap:fiat_object_part for the root level NIF classes
    • Classes under both BFO’s snap: fiat_object_part and snap:object have been moved directly under ‘Material_entity’
    • Addition of alternate labels for the roots of each of the NIFSTD modules
  • Additional partomoy restrictions within NIF-Anatomy. Additional classes from NeuroLex wiki
  • Additional restrictions for neuron by (by their soma location) brain region classification.
  • Inclusion of NIF-Cell-Molecule-Role-Bridge to assert restrictions to classify neuron by their circuit roles, i.e., intrinsic neuron role or principal neuron roles
  • Additional restrictions in NIF-Molecule-role bridging module

NIFSTD Release 1.7

  • Retirement of OBO-UBO layer:Eliminated the need of BIRNLex-OBO-UBO module (a common bridge between all NIF modules and BFO) to be imported
    • The upper level classes from BIRNLex-OBO-UBO are all moved to their appropriate domain specific modules. This allows the NIFSTD modules to be loaded directly under BFO entities
    • Classes from BIRNLex-OBO-UBO have been retired and replaced (using isReplacedByClass annotation property) with the module specific new Class IDs
    • Upper level hierarchies within the NIF modules have been significantly simplified and normalized under BFO
  • Content Enhancement and Improvements:
    • Inclusion of Protein Ontology (PRO)under NIF-Molecule module.
    • Molecules hierarchy has been modified to reflect close alignment between NIF’s Chemical and CHEBI’s upper level hierarchies
    • More neuron labels are altered in NIF-Cell module to conform with standardized naming convention by NIF cell working group
    • Additional partonomy relations for NIF-Anatomy
    • New classes and annotations from NeuroLex wiki contributions in different modules

NIFSTD Release 1.4

  • Enforced Modularity:Modularity principles have been vastly improved in the current  version
    • The dependencies between the modules have been reduced to a minimum; the modules can be simply loaded independently under just the upper level BFO ontologies
    • Classes from SAO ontology have been placed  under the appropriate modules
    • Modules have been normalized to create cleaner and more intuitive hierarchies
  • Elimination of duplicate classes: Due to multiple overlapping imports, version 0.5-1.0 had various duplicate classes which have been eliminated in the current version
  • Content Enhancements and Additional Modules:  600+ classes have been newly addedand 550+ classes have been enhanced with new annotations  based on NeuroLex contributions.
    • NIF-Chemical module (reusing neuroscience literature keyword terms and their hierarchy from CHEBI ontology)  has been added under NIF-Molecule
    • NIF-BioProcess includes GO’s Biological Process ontology as a separate module
    • NIF-Resourcemodule which contains high level resource descriptor class types such as Data, Software, Materials, Service, Education, Funding, Job, and People.
      • Contains logical restrictions to infer any needed existing classes from NIF-Investigation module. Also includes human friendly labels as needed for NIF’s curators
  • Enhanced Partonomy Relations:Brain region partonomy within the NIF-Anatomy module has been vastly enhanced with additional part_of/ has_part restrictions
    • Current partomonies can be best viewed through NeuroLex wiki from here .
  • Standardized Neuron Names: Many of the old neuron type labels in  NIF-Cell module have been updated with standardized naming conventions as proposed by NIF Cell Working Group.
  • Neuron by Neurotransmitter Classification: Based on NeuroLex wiki contributions by NIF cell working group, a bridge file has been constructed between NIF-Cell and NIF-Molecule to assert relation between a neuron and its neurotransmitter.
  • Neuron by Brain Region: A bridge file between NIF-Cell and NIF-Anatomy is being under construction which asserts restrictions to provide an inferred  classification of neurons based on their soma location in different brain regions.

NIFSTD Release 1.0

  • Version: 1.0, Date: January 25, 2009; Previous major release: NIFSTD 0.5
  • Location of the main interface owl file with all the imports for NIF 1.0 can be found at http://ontology.neuinfo.org/NIF/Archive/Feb-11-2009/nif.owl
  • NIF ontologies have been modularized into smaller units that are intended to be orthogonal to one another
    • The SAO classes have been re-organized and placed appropriately under the new NIF modules (e.g., Cell, Molecule, Subcellular , Organism and GrossAnatomy etc.)
    • The main import hierarchy has been simplified to avoid redundant loading of upper-level ontologies as it was in NIF 0.5
    • Loading individual ontologies requires the nif_backend.owl to be loaded first to have the ontologies constructed under the upper level formal ontologies
  • New convention for class identifiers
    • Any extensions added by NIF to an imported ontology are identified by the nif_ext prefix (NIF extension)** If an imported ontology was not OBO compliant, e.g., used a string as a class name, was not in OWL or had to be refactored according to BFO, NIF assigns its own class name, and the mapping to the source concept is maintained through the annotation properties, e.g, NeuroNamesID: 342
    • The prefix to be used by NIF will be nlx (NeuroLex) followed by an extension that indicates the core module,e.g., cell, anatomy etc. The following prefixes are used: nlx_cell, nlx_subcell, nlx_anat, nlx_mol, nlx_inv, nlx_res, nlx_dys (NIF dysfunction), nlx_fnc (NIF Function)
  • Added new contents
    • Incorporated approved changes recommended in the NeuroLex Wiki: (new classes, enhanced annotation, corrections etc.) from October 2nd to end of December (http://ontology.neuinfo.org/NIF/1.0/WikiChanges_1.htm)
    • From Cerebellum ontology which was developed by an intern student supervised by Dr. Maryann Martone. The new classes are added into NIF-GrossAnatomy.owl
    • NIF-Resource module: NIFSTD currently lists resource descriptors, e.g., software etc., under NIF Investigation. For the future release, we created this separate module, the NIF Resource module, to cover those concepts. This module will fix the set of high level descriptors, adding classes like "service", and also attempt to harmonize the Biomedical Resource Ontology (BRO), NITRC resource descriptors and OBI classes
    • The newly added classes can be tracked by searching the identifiers prefixed with nlx_cell_x, nlx_anat_x,nlx_subcell, nlx_inv etc. where x represents the creation date (year and month) of the term followed by a number. For example, nlx_cell_20081201 represents the first class id created in the month of December 2008 for NIF_Cell onology. This format will enable us to have an fast and easy list of terms added in a particular month grouped by a specific module for monthly update reports
    • A total of 96 new classes and 45+ new annotations/corrections have been added into different modules.
  • Resolved technical issues for Protege 3.X
    • Displaying the class labels for the ontologies converted from obo format
    • Displaying individual meta-date information for each of the ontologies when loaded together under the main hierarchy
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