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From: <al...@us...> - 2007-07-06 08:22:21
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Revision: 94
http://obi.svn.sourceforge.net/obi/?rev=94&view=rev
Author: alanr
Date: 2007-07-06 01:22:24 -0700 (Fri, 06 Jul 2007)
Log Message:
-----------
Raw import, edited by alan to fix namespaces, remove some extraneous quotation marks. Created from version emailed from Trish on July 5
Modified Paths:
--------------
branchDevelopment/trunk/Biomaterial.owl
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From: <dan...@us...> - 2007-08-17 16:27:55
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Revision: 133
http://obi.svn.sourceforge.net/obi/?rev=133&view=rev
Author: daniel_schober
Date: 2007-08-17 09:27:56 -0700 (Fri, 17 Aug 2007)
Log Message:
-----------
DS: This branch was made compliant to the naming conventions
NC examples:
Library , OBI_1000003 was renamed screening_library, library was made alternative tern.
Whole mount, OBI_1000049 was renamed whole_mount_preparation
NaturalBiomaterialEntity was renamed natural_biomaterial (removing tabooword)
Plasma was renamed blood_plasma
PBS to PBS_buffer
Here the changeTab report:
Composite Change Create subclass of type owl:Class -- Apply to: Class_1 schober 08/14/2007 16:24:44 BST
Superclass Added Superclass Added: flow_cytometer_analyzer (added to: flow_cytometer_sorter) schober 08/14/2007 16:25:28 BST
Composite Change Annotation Added: rdfs:label: '' to class: OBI_400134 schober 08/14/2007 16:25:28 BST
Subclass Added Subclass Added: OBI_400134 (added to: flow_cytometer_analyzer) schober 08/14/2007 16:25:28 BST
Composite Change Remove superclass schober 08/14/2007 16:25:28 BST
Superclass Added Superclass Added: instrument (added to: flow_cytometer_analyzer) schober 08/14/2007 16:26:20 BST
Subclass Added Subclass Added: OBI_400008 (added to: instrument) schober 08/14/2007 16:26:20 BST
Composite Change Remove superclass schober 08/14/2007 16:26:20 BST
Composite Change Delete class schober 08/14/2007 16:27:35 BST
Superclass Added Superclass Added: ?flow_cytometer (added to: flow_cytometer_analyzer) schober 08/14/2007 16:28:54 BST
Subclass Added Subclass Added: OBI_400008 (added to: ?flow_cytometer) schober 08/14/2007 16:28:54 BST
Composite Change Remove superclass schober 08/14/2007 16:28:54 BST
Composite Change Create subclass of type owl:Class -- Apply to: Class_2 schober 08/14/2007 16:29:03 BST
Composite Change Create subclass of type owl:Class -- Apply to: Class_3 schober 08/14/2007 16:29:54 BST
Composite Change Delete class schober 08/14/2007 16:29:59 BST
Composite Change Create subclass of type owl:Class -- Apply to: Class_4 schober 08/14/2007 16:30:03 BST
Superclass Added Superclass Added: cytometer (added to: image_cytometer) schober 08/14/2007 16:30:19 BST
Composite Change Annotation Added: rdfs:label: '' to class: OBI_400137 schober 08/14/2007 16:30:19 BST
Subclass Added Subclass Added: OBI_400135 (added to: cytometer) schober 08/14/2007 16:30:19 BST
Composite Change Remove superclass schober 08/14/2007 16:30:19 BST
Superclass Added Superclass Added: cytometer (added to: ?flow_cytometer) schober 08/14/2007 16:30:25 BST
Subclass Added Subclass Added: OBI_400044 (added to: cytometer) schober 08/14/2007 16:30:25 BST
Composite Change Remove superclass schober 08/14/2007 16:30:25 BST
Composite Change Annotation Added: editor_note: '' to class: OBI_48 schober 08/14/2007 16:38:37 BST
Composite Change Annotation Added: rdfs:label: '~#en liquid_chromatography_instrument' to class: OBI_48 schober 08/14/2007 16:42:37 BST
Composite Change Annotation Added: rdfs:label: 'polystyrene_tube' to class: OBI_10000004 schober 08/14/2007 16:45:04 BST
Superclass Added Superclass Added: fiat_object_part (added to: InstrumentAndPart_temporary) schober 08/14/2007 16:51:28 BST
Composite Change Annotation Added: rdfs:label: 'supernatant_collection_system_harvesting_frame' to class: OBI_10000008 schober 08/14/2007 16:51:28 BST
Subclass Added Subclass Added: OBI_400133 (added to: fiat_object_part) schober 08/14/2007 16:51:28 BST
Composite Change Remove superclass schober 08/14/2007 16:51:28 BST
Superclass Added Superclass Added: artefact_object (added to: InstrumentAndPart_temporary) schober 08/14/2007 16:53:29 BST
Subclass Added Subclass Added: OBI_400133 (added to: artefact_object) schober 08/14/2007 16:53:29 BST
Composite Change Remove superclass schober 08/14/2007 16:53:29 BST
Composite Change Create subclass of type owl:Class -- Apply to: Class_5 schober 08/14/2007 17:23:53 BST
Composite Change Annotation Added: rdfs:label: '' to class: OBI_400138 schober 08/14/2007 17:25:24 BST
Superclass Added Superclass Added: _move_to_biomaterial_branch (added to: ?sheath_fluid) schober 08/14/2007 17:25:50 BST
Composite Change Annotation Added: editor_note: 'DS: Is a fluid an instrument? Or even part of an instrument ?
All: All fluids and the propellant/ gas should be submitted to the material branch. or role?' to class: OBI_400090 schober 08/14/2007 17:25:50 BST
Subclass Added Subclass Added: OBI_400092 (added to: _move_to_biomaterial_branch) schober 08/14/2007 17:25:50 BST
Composite Change Remove superclass schober 08/14/2007 17:25:50 BST
Superclass Added Superclass Added: _move_to_biomaterial_branch (added to: ?sample_fluid) schober 08/14/2007 17:26:45 BST
Subclass Added Subclass Added: OBI_400090 (added to: _move_to_biomaterial_branch) schober 08/14/2007 17:26:45 BST
Composite Change Remove superclass schober 08/14/2007 17:26:45 BST
Superclass Added Superclass Added: _move_to_biomaterial_branch (added to: ?sheath_propellent) schober 08/14/2007 17:26:48 BST
Subclass Added Subclass Added: OBI_400093 (added to: _move_to_biomaterial_branch) schober 08/14/2007 17:26:48 BST
Composite Change Remove superclass schober 08/14/2007 17:26:48 BST
Annotation Added Annotation Added: editor_note: '' to class: OBI_400072 schober 08/17/2007 14:00:20 BST
Composite Change Annotation Modified: annotation editor_note for class: OBI_40 set to: [syn: mobile_phase] schober 08/17/2007 14:00:20 BST
Composite Change Annotation Added: preferred_term: '?manufacturer_of_flow_cytometer' to class: OBI_400072 schober 08/17/2007 14:03:00 BST
Composite Change Annotation Added: editor_note: 'DS: I guess this must go under Manufacturer. I also would opt for flow_cytometer_manufactrer insted (keep one convention consistently). At the end I am sure this will be an unnamed class or just a property of flow_cytometer.' to class: OBI_400072 schober 08/17/2007 14:36:17 BST
Composite Change Annotation Added: rdfs:label: '~#en ?manufacturer_of_flow_cytometer' to class: OBI_400072 schober 08/17/2007 14:36:38 BST
Composite Change Annotation Added: preferred_term: 'avalanche_photodiode' to class: OBI_400011 schober 08/17/2007 14:36:52 BST
Composite Change Annotation Added: rdfs:label: '~#en avalanche_photodiode' to class: OBI_400011 schober 08/17/2007 14:37:39 BST
Composite Change Annotation Added: preferred_term: 'voltage_amplifier' to class: OBI_400101 schober 08/17/2007 14:38:03 BST
Superclass Added Superclass Added: _move_to_biomaterial_branch (added to: ?column_chromatography_solvent) schober 08/17/2007 14:40:16 BST
Composite Change Annotation Added: rdfs:label: '~#en voltage_amplifier' to class: OBI_400101 schober 08/17/2007 14:40:16 BST
Subclass Added Subclass Added: OBI_40 (added to: _move_to_biomaterial_branch) schober 08/17/2007 14:40:16 BST
Composite Change Remove superclass schober 08/17/2007 14:40:16 BST
Superclass Added Superclass Added: _collected_relations (added to: ?manufacturer_of_flow_cytometer) schober 08/17/2007 14:43:13 BST
Subclass Added Subclass Added: OBI_400072 (added to: _collected_relations) schober 08/17/2007 14:43:13 BST
Composite Change Remove superclass schober 08/17/2007 14:43:14 BST
Composite Change Annotation Added: owl:versionInfo: 'TODO: ' to class: OBI_10000002 schober 08/17/2007 14:47:05 BST
Composite Change Annotation Added: editor_note: '' to class: OBI_10000002 schober 08/17/2007 14:59:50 BST
Composite Change Annotation Added: editor_note: '' to class: OBI_400120 schober 08/17/2007 15:21:18 BST
Superclass Added Superclass Added: labware (added to: waterbath) schober 08/17/2007 15:21:22 BST
Composite Change Annotation Added: rdfs:label: '?filtration_instrument' to class: OBI_10000007 schober 08/17/2007 15:21:22 BST
Subclass Added Subclass Added: OBI_400120 (added to: labware) schober 08/17/2007 15:21:22 BST
Composite Change Remove superclass schober 08/17/2007 15:21:22 BST
Annotation Removed Annotation Removed: editor_note from class: waterbath schober 08/17/2007 15:21:49 BST
Annotation Added Annotation Added: editor_note: 'DS: Is a waterbath labware or an instrument?' to class: OBI_400120 schober 08/17/2007 15:21:49 BST
Name Changed Name change from 'toBeDiscussed' to 'biomaterial_temporary' schober 08/17/2007 16:45:46 BST
Name Changed Name change from 'ExperimentalBiomateralEntity' to 'experimental_biomateral_entity' schober 08/17/2007 16:57:07 BST
Composite Change Annotation Added: editor_note: '' to class: experimental_biomateral_entity schober 08/17/2007 17:00:28 BST
Composite Change Annotation Added: preferred_term: 'cell_culture' to class: OBI_1000000 schober 08/17/2007 17:00:34 BST
Composite Change Annotation Added: rdfs:label: '~#en cell_culture' to class: OBI_1000000 schober 08/17/2007 17:01:10 BST
Composite Change Annotation Added: preferred_term: 'synthetic_polypeptide' to class: OBI_1000015 schober 08/17/2007 17:01:20 BST
Composite Change Annotation Added: rdfs:label: '~#en synthetic_polypeptide' to class: OBI_1000015 schober 08/17/2007 17:01:43 BST
Composite Change Annotation Added: preferred_term: 'bronchial_aveolar_lavage' to class: OBI_1000020 schober 08/17/2007 17:01:53 BST
Composite Change Annotation Added: rdfs:label: '~#en bronchial_aveolar_lavage' to class: OBI_1000020 schober 08/17/2007 17:02:04 BST
Composite Change Annotation Added: alternative_term: '' to class: OBI_1000020 schober 08/17/2007 17:02:27 BST
Composite Change Annotation Added: preferred_term: 'cDNA_library' to class: OBI_1000021 schober 08/17/2007 17:02:46 BST
Composite Change Annotation Added: rdfs:label: '~#en cDNA_library' to class: OBI_1000021 schober 08/17/2007 17:03:48 BST
Composite Change Annotation Added: preferred_term: 'phage_display_library' to class: OBI_1000029 schober 08/17/2007 17:04:02 BST
Composite Change Annotation Added: rdfs:label: '~#en phage_display_library' to class: OBI_1000029 schober 08/17/2007 17:04:16 BST
Composite Change Annotation Added: alternative_term: '' to class: OBI_1000029 schober 08/17/2007 17:05:19 BST
Composite Change Annotation Added: preferred_term: 'screening_library' to class: OBI_1000003 schober 08/17/2007 17:05:31 BST
Composite Change Annotation Added: rdfs:label: '~#en screening_library' to class: OBI_1000003 schober 08/17/2007 17:07:22 BST
Annotation Added Annotation Added: alternative_term: '' to class: OBI_1000049 schober 08/17/2007 17:08:01 BST
Composite Change Annotation Added: editor_note: 'original term: protein fragment split into synthetic polypeptide and fragment derived from protein
DS: Is this synthetic an oxymoron to the biomaterial?' to class: OBI_1000015 schober 08/17/2007 17:08:01 BST
Composite Change Annotation Added: example_of_usage: 'whole_mount' to class: OBI_1000049 schober 08/17/2007 17:08:06 BST
Composite Change Annotation Added: alternative_term: 'whole_mount' to class: OBI_1000049 schober 08/17/2007 17:08:18 BST
Composite Change Annotation Added: preferred_term: 'whole_mount_preparation' to class: OBI_1000049 schober 08/17/2007 17:08:31 BST
Composite Change Annotation Added: example_of_usage: 'whole_mount_preparation' to class: OBI_1000049 schober 08/17/2007 17:08:50 BST
Name Changed Name change from 'geneticInformationContent' to 'genetic_information_content' schober 08/17/2007 17:10:13 BST
Composite Change Annotation Added: rdfs:label: '~#en whole_mount_preparation' to class: OBI_1000049 schober 08/17/2007 17:10:13 BST
Composite Change Annotation Added: editor_note: '' to class: genetic_information_content schober 08/17/2007 17:11:14 BST
Annotation Added Annotation Added: editor_note: '' to class: NaturalBiomaterialEntity schober 08/17/2007 17:11:43 BST
Composite Change Annotation Modified: annotation editor_note for class: experimental_biomateral_entity set to: [DS: what is this? Does the 'experimental' here refer to the biomaterials role in an experiment? Or does this refer to the metadata level, e.g. indicating this class' experimental status?, ] schober 08/17/2007 17:11:43 BST
Name Changed Name change from 'NaturalBiomaterialEntity' to 'natural_biomaterial' schober 08/17/2007 17:12:17 BST
Composite Change Annotation Added: editor_note: 'DS: Assign metadata and ID' to class: natural_biomaterial schober 08/17/2007 17:13:12 BST
Composite Change Annotation Added: preferred_term: 'unicellular_organism' to class: OBI_1000007 schober 08/17/2007 17:13:25 BST
Superclass Added Superclass Added: organism (added to: chimera) schober 08/17/2007 17:14:10 BST
Composite Change Annotation Added: rdfs:label: '~#en unicellular_organism' to class: OBI_1000007 schober 08/17/2007 17:14:10 BST
Subclass Added Subclass Added: chimera (added to: organism) schober 08/17/2007 17:14:10 BST
Composite Change Remove superclass schober 08/17/2007 17:14:11 BST
Composite Change Annotation Added: preferred_term: 'blood_plasma' to class: OBI_1000017 schober 08/17/2007 17:14:44 BST
Composite Change Annotation Added: rdfs:label: '~#en blood_plasma' to class: OBI_1000017 schober 08/17/2007 17:14:51 BST
Composite Change Annotation Added: alternative_term: '' to class: OBI_1000017 schober 08/17/2007 17:16:29 BST
Composite Change Annotation Added: preferred_term: 'cell_derived_from_multicellular_organism' to class: OBI_1000001 schober 08/17/2007 17:16:35 BST
Composite Change Annotation Added: rdfs:label: '~#en cell_derived_from_multicellular_organism' to class: OBI_1000001 schober 08/17/2007 17:16:45 BST
Composite Change Annotation Added: preferred_term: 'immortal_cell' to class: OBI_1000002 schober 08/17/2007 17:16:49 BST
Composite Change Annotation Added: rdfs:label: '~#en immortal_cell' to class: OBI_1000002 schober 08/17/2007 17:17:15 BST
Composite Change Annotation Added: preferred_term: 'artificially_engineered_biomaterial' to class: OBI_1000012 schober 08/17/2007 17:17:59 BST
Composite Change Annotation Added: editor_note: 'added as hierarchy term
DS: I guess this is an alternative term for object!' to class: OBI_1000005 schober 08/17/2007 17:18:18 BST
Composite Change Annotation Added: rdfs:label: '~#en sf' to class: OBI_1000012 schober 08/17/2007 17:18:53 BST
Composite Change Annotation Added: preferred_term: 'fragment_derived_from_protein' to class: OBI_1000014 schober 08/17/2007 17:18:56 BST
Composite Change Annotation Added: rdfs:label: '~#en fragment_derived_from_protein' to class: OBI_1000014 schober 08/17/2007 17:19:28 BST
Composite Change Annotation Added: preferred_term: 'liquid_chemical_solution' to class: OBI_1000004 schober 08/17/2007 17:19:32 BST
Composite Change Annotation Added: rdfs:label: '~#en liquid_chemical_solution' to class: OBI_1000004 schober 08/17/2007 17:19:55 BST
Composite Change Annotation Added: preferred_term: 'PBS_buffer' to class: OBI_1000041 schober 08/17/2007 17:20:01 BST
Composite Change Annotation Added: rdfs:label: '~#en PBS_buffer' to class: OBI_1000041 schober 08/17/2007 17:21:50 BST
Composite Change Annotation Added: editor_note: 'huh? Status does not sound like a material
DS: exactly. Push to relevant branch.' to class: OBI_1000040 schober 08/17/2007 17:22:03 BST
Composite Change Annotation Added: preferred_term: '?organism_status' to class: OBI_1000040 schober 08/17/2007 17:22:13 BST
Composite Change Annotation Added: rdfs:label: '~#en ?organism_status' to class: OBI_1000040 schober 08/17/2007 17:22:55 BST
Composite Change Annotation Added: rdfs:label: '~#en ChEBI_object' to class: OBI_336 schober 08/17/2007 17:23:09 BST
Composite Change Annotation Added: rdfs:label: 'Triton_X-100' to class: OBI_10000006 schober 08/17/2007 17:23:20 BST
Superclass Added Superclass Added: biomaterial_temporary (added to: ChEBI_object) schober 08/17/2007 17:24:09 BST
Composite Change Annotation Added: rdfs:label: '?chromium_51' to class: OBI_10000009 schober 08/17/2007 17:24:09 BST
Subclass Added Subclass Added: OBI_336 (added to: biomaterial_temporary) schober 08/17/2007 17:24:09 BST
Composite Change Remove superclass schober 08/17/2007 17:24:09 BST
Modified Paths:
--------------
branchDevelopment/trunk/Biomaterial.owl
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From: <dan...@us...> - 2007-10-04 15:59:23
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Revision: 157
http://obi.svn.sourceforge.net/obi/?rev=157&view=rev
Author: daniel_schober
Date: 2007-10-04 08:58:49 -0700 (Thu, 04 Oct 2007)
Log Message:
-----------
The following terms as submitted by the PA branch were added.
"General comments on the biomaterial branch: Many classes do not have label and preferred_label both set. Some , especially the helper classes are without IDs. I marked questionable classes with a '?', and put my issues in the editor note annotation property."
Comment Schober parent_term / where does it go preferred_term definition example editor_note source branch / community
put under cell culture biomaterial primary cell culture cells put directly into culture from a tissue source spleen cells put directly into culture Protocol App Branch
put under cell culture biomaterial cell line culture long term culture of cells that are replicating continuosly. The cell population is homogenous but not clonal HeLa cells Protocol App Branch
put under cell culture biomaterial clonal cell culture "cell culture in which all cells can be assumed to be identical, tracking back to a single ancestor cell" cell cut KPC
"Put under cell component, but may be alternative term for that." biomaterial cellular compartment part of a cell enlosed by a membrane cytosol KPC
Put under enzyme Biomaterial / Reagent DNA polymerase An enzyme which facilitates the copying of DNA. Taq polymerase is a commonly used DNA polymerase to copy DNA templates in PCR reactions. KPC
Put under biological_macromolecule biomaterial / reagent enzyme A protein which mediates a defined chemical reaction to one or more target molecules A protease is an enzyme which catalyses the breakdown of proteins into smaller peptides. KPC
Probably pass to roles branch biomaterial / reagent Bead A globular or round particle of defined physicochemical properties and size which can be exploited as either the primary substance for detection or as a secondary solid platform for the attachment of bioactive molecules Dynabeads are commercially available magnetic beads which are precoated with antibodies specific for select cellular receptors and are used to separate cell populations. KPC
Pass to Instruments/labware branch biomaterial / reagent dialysis membrane a semi permeable membrance with known pore size A dialysis membrane of pore size 1000 Da MWCO is used to separate molecules of greater than 1000 Da MWCO from those which are less than 1000 Da MWCO. KPC
Put under artificially_engineered_biomaterial biomaterial / reagent cloning vector "a autonomous replicating vehicle, such as a plasmid or virus vector, which can be modified by the insertion of foreign DNA and when introduced into recipient cells does not alter the viability of those cells" The DNA expressing the protein of interest was inserted within pM13 which was then transfected into a cell line to facilitate expression of the protein. KPC
Put under experimental biomaterial. Probably a role? biomaterial / reagent dye A substance capable of staining or coloring defined targets Acridine orange is a nucleic acid selective dye. KPC
Put under enzyme biomaterial / reagent reverse transcriptase "an enzyme that faciliatates the conversion of RNA to DNA. May be natural, recombinant or modified" Avian reverse transcriptase transcribes RNA into complementary DNA. KPC
Modified Paths:
--------------
branchDevelopment/trunk/Biomaterial.owl
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From: <jam...@us...> - 2008-01-10 13:30:36
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Revision: 237
http://obi.svn.sourceforge.net/obi/?rev=237&view=rev
Author: jamesmalone
Date: 2008-01-10 05:30:42 -0800 (Thu, 10 Jan 2008)
Log Message:
-----------
Update to IDs and meta data.
Modified Paths:
--------------
branchDevelopment/trunk/Biomaterial.owl
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From: <mco...@us...> - 2008-01-10 20:10:55
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Revision: 240
http://obi.svn.sourceforge.net/obi/?rev=240&view=rev
Author: mcourtot
Date: 2008-01-10 12:11:00 -0800 (Thu, 10 Jan 2008)
Log Message:
-----------
===================OBI_100000===================
Added example of usage
================================================
===================OBI_100006===================
================================================
===================OBI_100058===================
Added example of usage
================================================
===================OBI_100036===================
================================================
===================OBI_100034===================
================================================
===================OBI_100002===================
Added example of usage
================================================
===================OBI_100005===================
================================================
===================OBI_100003===================
================================================
===================OBI_100004===================
================================================
===================OBI_100007===================
Added definition
Added example of usage
================================================
===================OBI_100020===================
================================================
===================OBI_100009===================
================================================
===================OBI_100011===================
Added example of usage
================================================
===================OBI_100010===================
Added example of usage
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===================OBI_100018===================
================================================
===================OBI_100019===================
================================================
===================OBI_100022===================
Added preferred term
================================================
===================OBI_100023===================
Added example of usage
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===================OBI_100025===================
================================================
===================OBI_100024===================
================================================
===================OBI_100021===================
================================================
===================OBI_100015===================
================================================
===================OBI_100016===================
================================================
===================OBI_100017===================
================================================
===================OBI_100012===================
================================================
===================OBI_100026===================
Added example of usage
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===================OBI_100030===================
Added example of usage
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===================OBI_100029===================
Added example of usage
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===================OBI_100031===================
Added example of usage
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===================OBI_100027===================
================================================
===================OBI_100032===================
Added example of usage
================================================
===================OBI_100028===================
Added example of usage
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===================OBI_100008===================
================================================
===================OBI_100013===================
================================================
===================OBI_100014===================
Added example of usage
Added definition source
================================================
===================OBI_100040===================
================================================
===================OBI_100037===================
================================================
===================OBI_100038===================
================================================
===================OBI_100051===================
Added example of usage
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===================OBI_100055===================
Added example of usage
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===================OBI_100056===================
Added example of usage
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===================OBI_100053===================
Added example of usage
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===================OBI_100054===================
================================================
===================OBI_100052===================
Added example of usage
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===================OBI_100057===================
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===================_unclassified===================
Added preferred term
Added example of usage
Added curation_status
Added definition source
================================================
===================OBI_1000035===================
================================================
===================OBI_100059===================
Added example of usage
Added curation_status
================================================
===================OBI_1000036===================
================================================
===================OBI_1000029===================
================================================
===================OBI_1000042===================
================================================
===================OBI_100064===================
================================================
===================OBI_100066===================
================================================
===================OBI_1000023===================
================================================
===================OBI_100065===================
================================================
===================OBI_1000209===================
Added curation_status
Added definition editor
Added definition source
================================================
===================OBI_100060===================
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===================OBI_100061===================
================================================
===================OBI_100063===================
================================================
===================OBI_100062===================
================================================
===================OBI_1000048===================
================================================
===================OBI_100067===================
================================================
===================OBI_1000021===================
================================================
===================OBI_1000024===================
================================================
===================OBI_1000207===================
Added curation_status
Added definition editor
Added definition source
================================================
===================OBI_1000049===================
================================================
===================OBI_100050===================
================================================
===================OBI_1000005===================
================================================
===================OBI_336===================
Added preferred term
Added example of usage
Added curation_status
Added definition editor
Added definition source
================================================
===================OBI_10000006===================
Added preferred term
Added definition
Added example of usage
Added curation_status
Added definition editor
Added definition source
================================================
===================OBI_10000009===================
Added preferred term
Added definition
Added example of usage
Added curation_status
Added definition editor
Added definition source
================================================
===================OBI_100033===================
Added definition
Added example of usage
================================================
===================OBI_100041===================
================================================
===================OBI_100042===================
================================================
===================OBI_100039===================
================================================
===================OBI_100035===================
================================================
===================OBI_100043===================
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===================OBI_100044===================
================================================
===================OBI_100049===================
================================================
===================OBI_100045===================
================================================
===================OBI_100046===================
================================================
===================OBI_100048===================
================================================
===================OBI_100047===================
================================================
Modified Paths:
--------------
branchDevelopment/trunk/Biomaterial.owl
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From: <mco...@us...> - 2008-01-14 21:41:33
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Revision: 244
http://obi.svn.sourceforge.net/obi/?rev=244&view=rev
Author: mcourtot
Date: 2008-01-14 13:41:39 -0800 (Mon, 14 Jan 2008)
Log Message:
-----------
cleaned up organism sub branch:
virus
viroid
archaea
bacterium
deleted virus which was duplicated
Modified Paths:
--------------
branchDevelopment/trunk/Biomaterial.owl
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From: <mco...@us...> - 2008-01-14 21:49:33
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Revision: 245
http://obi.svn.sourceforge.net/obi/?rev=245&view=rev
Author: mcourtot
Date: 2008-01-14 13:49:34 -0800 (Mon, 14 Jan 2008)
Log Message:
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cleaned up enzyme sub branch
enzyme
DNA polymerase
reverse transcriptase
Modified Paths:
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branchDevelopment/trunk/Biomaterial.owl
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From: <mco...@us...> - 2008-01-14 22:28:45
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Revision: 246
http://obi.svn.sourceforge.net/obi/?rev=246&view=rev
Author: mcourtot
Date: 2008-01-14 14:28:50 -0800 (Mon, 14 Jan 2008)
Log Message:
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cleaned up vector
cultivar
xenograft
haplotype
diplotype
allele
Modified Paths:
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branchDevelopment/trunk/Biomaterial.owl
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From: <mco...@us...> - 2008-01-14 22:32:39
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Revision: 247
http://obi.svn.sourceforge.net/obi/?rev=247&view=rev
Author: mcourtot
Date: 2008-01-14 14:32:42 -0800 (Mon, 14 Jan 2008)
Log Message:
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deleted duplicate organism
moved chimera under organism (the one I kept)
clean up ecotype
Modified Paths:
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branchDevelopment/trunk/Biomaterial.owl
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From: <mco...@us...> - 2008-01-14 23:13:59
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Revision: 248
http://obi.svn.sourceforge.net/obi/?rev=248&view=rev
Author: mcourtot
Date: 2008-01-14 15:14:03 -0800 (Mon, 14 Jan 2008)
Log Message:
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clean up blood plasma
blood serum
population
Modified Paths:
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branchDevelopment/trunk/Biomaterial.owl
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From: <mco...@us...> - 2008-01-14 23:28:30
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Revision: 249
http://obi.svn.sourceforge.net/obi/?rev=249&view=rev
Author: mcourtot
Date: 2008-01-14 15:28:34 -0800 (Mon, 14 Jan 2008)
Log Message:
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added Biomaterial proposed definition cf last call
Modified Paths:
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branchDevelopment/trunk/Biomaterial.owl
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From: <mco...@us...> - 2008-01-14 23:49:03
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Revision: 250
http://obi.svn.sourceforge.net/obi/?rev=250&view=rev
Author: mcourtot
Date: 2008-01-14 15:49:01 -0800 (Mon, 14 Jan 2008)
Log Message:
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cleaned up cell
added editor notes: flag for removal
cleaned up PBS buffer
Modified Paths:
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branchDevelopment/trunk/Biomaterial.owl
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From: <jam...@us...> - 2008-01-15 15:56:36
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Revision: 259
http://obi.svn.sourceforge.net/obi/?rev=259&view=rev
Author: jamesmalone
Date: 2008-01-15 07:56:41 -0800 (Tue, 15 Jan 2008)
Log Message:
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Hierarchy changes to ontology - not finalised and require discussion on next call. JM
Modified Paths:
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branchDevelopment/trunk/Biomaterial.owl
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From: <mco...@us...> - 2008-01-15 23:09:34
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Revision: 260
http://obi.svn.sourceforge.net/obi/?rev=260&view=rev
Author: mcourtot
Date: 2008-01-15 15:09:36 -0800 (Tue, 15 Jan 2008)
Log Message:
-----------
clean up
added few editor notes
Modified Paths:
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branchDevelopment/trunk/Biomaterial.owl
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From: <mco...@us...> - 2008-01-15 23:45:05
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Revision: 261
http://obi.svn.sourceforge.net/obi/?rev=261&view=rev
Author: mcourtot
Date: 2008-01-15 15:45:11 -0800 (Tue, 15 Jan 2008)
Log Message:
-----------
clean up
updated curation status in the branch
Modified Paths:
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branchDevelopment/trunk/Biomaterial.owl
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From: <jam...@us...> - 2008-01-21 14:57:52
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Revision: 278
http://obi.svn.sourceforge.net/obi/?rev=278&view=rev
Author: jamesmalone
Date: 2008-01-21 06:57:57 -0800 (Mon, 21 Jan 2008)
Log Message:
-----------
Clean up of IDs and population concept removed. JM
Modified Paths:
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branchDevelopment/trunk/Biomaterial.owl
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From: <al...@us...> - 2008-02-01 00:51:42
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Revision: 290
http://obi.svn.sourceforge.net/obi/?rev=290&view=rev
Author: alanr
Date: 2008-01-31 16:51:47 -0800 (Thu, 31 Jan 2008)
Log Message:
-----------
Added Material
Modified Paths:
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branchDevelopment/trunk/Biomaterial.owl
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From: <al...@us...> - 2008-02-08 23:04:48
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Revision: 298
http://obi.svn.sourceforge.net/obi/?rev=298&view=rev
Author: alanr
Date: 2008-02-08 15:04:51 -0800 (Fri, 08 Feb 2008)
Log Message:
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s/_defined_biomaterial/_defined_material/
Modified Paths:
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branchDevelopment/trunk/Biomaterial.owl
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From: <p_r...@us...> - 2008-02-10 20:53:05
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Revision: 302
http://obi.svn.sourceforge.net/obi/?rev=302&view=rev
Author: p_rocca_serra
Date: 2008-02-10 12:53:09 -0800 (Sun, 10 Feb 2008)
Log Message:
-----------
Modified Paths:
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branchDevelopment/trunk/Biomaterial.owl
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From: <al...@us...> - 2008-02-11 12:59:36
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Revision: 304
http://obi.svn.sourceforge.net/obi/?rev=304&view=rev
Author: alanr
Date: 2008-02-11 04:59:24 -0800 (Mon, 11 Feb 2008)
Log Message:
-----------
minor oops - edited _defined_biomaterial -> _defined_material , but missed one instance.
Modified Paths:
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branchDevelopment/trunk/Biomaterial.owl
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From: <p_r...@us...> - 2008-02-24 22:42:12
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Revision: 336
http://obi.svn.sourceforge.net/obi/?rev=336&view=rev
Author: p_rocca_serra
Date: 2008-02-24 14:42:07 -0800 (Sun, 24 Feb 2008)
Log Message:
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changes to BM file:
creation of _CHEBI_object import placeholder class
-moved from 'unclassified with its childern
-moved biomolecule class with its children under _CHEBI_object
creation of a class Collection (metadata to be added)
-moved Population class as a child of collection
-moved Sample-population as a child of population
-moved cDNA library, Phage display library as children of Collection
PRS: 22-02-2008: screening library (from previously unclassified) was temporarily placed there but
while working on definition of cDNA library and looking at example of usage for screening library, a screening library should be a defined class -> any material library which has input_role in a screening protocol application
Under biomaterial
creation of helper class _move to role?
creation of helper class _move to protocol application?
-moved genetic_modification
note: need to check/submit to PATO 'genetically modified' as a quality
creation of helper class _move to information_content_entity? -> submission to tracker Item 1899832
-moved Genotype
-moved strain
-moved serotype
-moved genetic information content
creation of helper class _move to site?
-moved in_vivo biomaterial
-need to add in-vitro biomaterial (this is following discussion during Vancouver Meeting)
creation of helper class, "?a defined class is needed" where we put
-moved natural and artificial material
-moved ecotype
NOTE1: post call during file review,by the same line of reasoning, decided to move class 'experimental biomaterial entity' and children there
OK with everyone ?
NOTE2: For all classes placed underneath, I have created an editor note with a possible statement for creating the defined class.
I have based the statement on the proposal made by Bjoern.
I have also created a google spreadsheet similar to that used by DT and fill in the blancks
I have to update to add objectives and constraints
creation of helper class "move to quality"
-moved 'immortal cell' from cell and submit 'immortal' to PATO
addition of role to the following classes
-cell entity
-blood plasma
-blood serum
-virus
-viroid
-cultivar
-molecular mixture
-entity of organismal origin
-xenograft
-cDNA library
-phage display library
-screening library (but pay attention to point made earlier)
NOTE3:
I have not added anything to biomolecule as more work is required (monomer is not necessarily a biomolecule)
QUESTIONS:
under chemical entity we have 'peptide and polypeptide'
under unclassified we have 'fragment derived from protein'
under experimental biomaterial entity we have 'synthetic polypeptide'
I believe the last 2 could be defined classes
synthetic peptide = a peptide with output_role during chemical synthesis protocol application
I have created a test defined class with a 'has_role some (has_role some output_role)' restriction but I don't how to capture protocol_application = chemical synthesis (which by the way is absent from PA)
On the same line, need from members of BM-branch to review the Material Transformation spreadsheet
During the creation of the spreadsheet,I have noted we were missing organs and tissues
I have therefore created placeholders under multicellular entity of organismal origin (OBI_100057) with a mapping to 2 CARO entries.
(This is to help keep track of the things we may need to import/slurp using the procedure outlined by Alan and documented by Melanie.)
Modified Paths:
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branchDevelopment/trunk/Biomaterial.owl
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From: <mco...@us...> - 2008-02-25 22:25:35
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Revision: 341
http://obi.svn.sourceforge.net/obi/?rev=341&view=rev
Author: mcourtot
Date: 2008-02-25 14:24:49 -0800 (Mon, 25 Feb 2008)
Log Message:
-----------
corrected restrictions on test_synthetic peptide
Modified Paths:
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branchDevelopment/trunk/Biomaterial.owl
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From: <al...@us...> - 2008-02-26 19:23:02
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Revision: 342
http://obi.svn.sourceforge.net/obi/?rev=342&view=rev
Author: alanr
Date: 2008-02-26 11:21:36 -0800 (Tue, 26 Feb 2008)
Log Message:
-----------
more spurious import statements - protege?
Modified Paths:
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branchDevelopment/trunk/Biomaterial.owl
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From: <al...@us...> - 2008-03-03 02:55:17
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Revision: 363
http://obi.svn.sourceforge.net/obi/?rev=363&view=rev
Author: alanr
Date: 2008-03-02 18:55:20 -0800 (Sun, 02 Mar 2008)
Log Message:
-----------
oops rdf:ID="OBI_1000024" should be rdf:about="http://obi.sourceforge.net/ontology/OBI.owl#OBI_1000024"
- accidentally slipped into wrong namespace because of this.
Modified Paths:
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branchDevelopment/trunk/Biomaterial.owl
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From: <mco...@us...> - 2008-03-04 22:21:04
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Revision: 378
http://obi.svn.sourceforge.net/obi/?rev=378&view=rev
Author: mcourtot
Date: 2008-03-04 14:20:47 -0800 (Tue, 04 Mar 2008)
Log Message:
-----------
updated cell label
Modified Paths:
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branchDevelopment/trunk/Biomaterial.owl
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