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From: <wh...@us...> - 2007-05-29 02:56:57
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Revision: 54
http://obi.svn.sourceforge.net/obi/?rev=54&view=rev
Author: whetzel
Date: 2007-05-28 19:56:59 -0700 (Mon, 28 May 2007)
Log Message:
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add updated file for Instrument ObiBranch
Modified Paths:
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branchDevelopment/trunk/InstrumentAndPart.owl
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From: <wh...@us...> - 2007-06-05 09:21:50
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Revision: 57
http://obi.svn.sourceforge.net/obi/?rev=57&view=rev
Author: whetzel
Date: 2007-06-05 02:21:52 -0700 (Tue, 05 Jun 2007)
Log Message:
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add terms from Excel Worksheet titled Ready2LoadTerms_05June2007.txt
Modified Paths:
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branchDevelopment/trunk/InstrumentAndPart.owl
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From: <wh...@us...> - 2007-06-05 17:54:18
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Revision: 61
http://obi.svn.sourceforge.net/obi/?rev=61&view=rev
Author: whetzel
Date: 2007-06-05 10:54:19 -0700 (Tue, 05 Jun 2007)
Log Message:
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new file generated after Instrument call, June 5, 2007
Modified Paths:
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branchDevelopment/trunk/InstrumentAndPart.owl
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From: <wh...@us...> - 2007-06-06 07:38:25
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Revision: 63
http://obi.svn.sourceforge.net/obi/?rev=63&view=rev
Author: whetzel
Date: 2007-06-06 00:38:26 -0700 (Wed, 06 Jun 2007)
Log Message:
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updated to ensure that proper input owl file was used for loading terms
Modified Paths:
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branchDevelopment/trunk/InstrumentAndPart.owl
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From: <wh...@us...> - 2007-06-22 02:01:09
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Revision: 79
http://obi.svn.sourceforge.net/obi/?rev=79&view=rev
Author: whetzel
Date: 2007-06-21 19:01:09 -0700 (Thu, 21 Jun 2007)
Log Message:
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try svn keyword for use with owl:versionInfo
Modified Paths:
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branchDevelopment/trunk/InstrumentAndPart.owl
Property Changed:
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branchDevelopment/trunk/InstrumentAndPart.owl
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From: <dan...@us...> - 2007-07-02 13:48:38
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Revision: 86
http://obi.svn.sourceforge.net/obi/?rev=86&view=rev
Author: daniel_schober
Date: 2007-07-02 06:48:33 -0700 (Mon, 02 Jul 2007)
Log Message:
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Marked questionable classes and added corresponding editor_notes, describing the problems.
Modified Paths:
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branchDevelopment/trunk/InstrumentAndPart.owl
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From: <dan...@us...> - 2007-07-03 16:27:45
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Revision: 87
http://obi.svn.sourceforge.net/obi/?rev=87&view=rev
Author: daniel_schober
Date: 2007-07-03 09:27:46 -0700 (Tue, 03 Jul 2007)
Log Message:
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Added annotation metadata to questionable positioned classes (?-prefixed), added administrative helper classes (_-prefixed).
Modified Paths:
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branchDevelopment/trunk/InstrumentAndPart.owl
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From: <dan...@us...> - 2007-10-16 16:20:36
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Revision: 165
http://obi.svn.sourceforge.net/obi/?rev=165&view=rev
Author: daniel_schober
Date: 2007-10-16 09:20:31 -0700 (Tue, 16 Oct 2007)
Log Message:
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added editor.note on instrument class (svn test)
Modified Paths:
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branchDevelopment/trunk/InstrumentAndPart.owl
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From: <mco...@us...> - 2007-12-06 23:19:34
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Revision: 201
http://obi.svn.sourceforge.net/obi/?rev=201&view=rev
Author: mcourtot
Date: 2007-12-06 15:19:38 -0800 (Thu, 06 Dec 2007)
Log Message:
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curated cyto_buoy family
Modified Paths:
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branchDevelopment/trunk/InstrumentAndPart.owl
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From: <mco...@us...> - 2007-12-07 00:59:15
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Revision: 203
http://obi.svn.sourceforge.net/obi/?rev=203&view=rev
Author: mcourtot
Date: 2007-12-06 16:59:20 -0800 (Thu, 06 Dec 2007)
Log Message:
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curated guava flow_cytometer_analyser family
Modified Paths:
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branchDevelopment/trunk/InstrumentAndPart.owl
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From: <mco...@us...> - 2007-12-07 19:41:08
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Revision: 204
http://obi.svn.sourceforge.net/obi/?rev=204&view=rev
Author: mcourtot
Date: 2007-12-07 11:41:08 -0800 (Fri, 07 Dec 2007)
Log Message:
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cleaned-up quotes and definition_source, except for flow cytometers instruments names (like BioSorter) that will be cleaned later
Modified Paths:
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branchDevelopment/trunk/InstrumentAndPart.owl
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From: <mco...@us...> - 2007-12-07 22:34:32
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Revision: 206
http://obi.svn.sourceforge.net/obi/?rev=206&view=rev
Author: mcourtot
Date: 2007-12-07 14:34:33 -0800 (Fri, 07 Dec 2007)
Log Message:
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curation continued
Modified Paths:
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branchDevelopment/trunk/InstrumentAndPart.owl
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From: <all...@us...> - 2007-12-11 13:56:06
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Revision: 212
http://obi.svn.sourceforge.net/obi/?rev=212&view=rev
Author: allysonlister
Date: 2007-12-11 05:55:52 -0800 (Tue, 11 Dec 2007)
Log Message:
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;; This buffer is for notes you don't want to save, and for Lisp evaluation.
;; If you want to create a file, first visit that file with C-x C-f,
;; then enter the text in that file's own buffer.
DNA_sequencer:
1. Didn't have curation_complete (had raw_import), but all fields were correctly filled in by Trish at the time. I've just updated the curation_complete, as this is a term with definition etc straight from MO.
2. Fixed typo in definition
array_scanner:
Same note as #1 in DNA_sequencer.
microarray_wash_station:
1. normalized definition. Now "A microarray wash station is an instrument used to wash Affymetrix-type arrays."
2. Question about the definition: it seems a very generic term, yet the definition specifies Affy arrays only. Shouldn't we generalize this definition, and then create a child of this which is only applicable to Affy arrays (if the latter is in fact required?)
crosslinking_instrument:
1. Question: if we intend that other ontologies can be used in conjunction with OBI, we shouldn't have such a general term used specifically for chemically joining two or more molecules. I'm sure there are other "crosslinkers" that are on a much different scale in engineering etc. I have modified the term as follows:
a. Preferred_name = molecular_crosslinker
Does everyone agree?
fluorometer: added to the definition, added curation_status and modified definition_source and _editor.
Modified Paths:
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branchDevelopment/trunk/InstrumentAndPart.owl
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From: <fgi...@us...> - 2008-01-07 14:23:43
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Revision: 235
http://obi.svn.sourceforge.net/obi/?rev=235&view=rev
Author: fgibson_sf
Date: 2008-01-07 06:23:32 -0800 (Mon, 07 Jan 2008)
Log Message:
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+Edits compliant with the Instument branch call https://wiki.cbil.upenn.edu/obiwiki/index.php/InstrumentMinutes11Dec2007
-moved analog-to-digital converter under instument
-deleted _collected relations and subclasses
-deleted instrumentAndPartTemporary and subclasses
-deleted column_chromatography_matrix and moved to biomaterial
-Added a definition and citation for chromatography column and moved it under labware
-moved electrophoresis_box under labware
-moved pump_valve_switch under labware
-deleted the class cardinal_part_of_fluidic_system and moved the subclasses under labware
Modified Paths:
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branchDevelopment/trunk/InstrumentAndPart.owl
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From: <dan...@us...> - 2008-02-12 17:38:42
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Revision: 311
http://obi.svn.sourceforge.net/obi/?rev=311&view=rev
Author: daniel_schober
Date: 2008-02-12 09:38:46 -0800 (Tue, 12 Feb 2008)
Log Message:
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cleaned up names, deleting Questionmarks in labels, e.g. # ?interrogation_point
# ?jet_in_air_flow_chamber
add AI into editor note for above.
Modified Paths:
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branchDevelopment/trunk/InstrumentAndPart.owl
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From: <dan...@us...> - 2008-02-19 13:40:24
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Revision: 327
http://obi.svn.sourceforge.net/obi/?rev=327&view=rev
Author: daniel_schober
Date: 2008-02-19 05:40:23 -0800 (Tue, 19 Feb 2008)
Log Message:
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obsoleted 'labware'(which we couldn't come up with a traceable nat lang definition) and moved its former children up, under 'device'
Modified Paths:
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branchDevelopment/trunk/InstrumentAndPart.owl
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From: <mco...@us...> - 2008-03-30 14:08:28
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Revision: 467
http://obi.svn.sourceforge.net/obi/?rev=467&view=rev
Author: mcourtot
Date: 2008-03-30 07:08:29 -0700 (Sun, 30 Mar 2008)
Log Message:
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corrected wrong instance of curation_status
normalized ID of droplet_sorter
Modified Paths:
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branchDevelopment/trunk/InstrumentAndPart.owl
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From: <all...@us...> - 2007-07-17 15:35:57
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Revision: 116
http://obi.svn.sourceforge.net/obi/?rev=116&view=rev
Author: allysonlister
Date: 2007-07-17 08:35:01 -0700 (Tue, 17 Jul 2007)
Log Message:
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Removed reagent from defintion of platform
Modified Paths:
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branchDevelopment/trunk/InstrumentAndPart.owl
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From: <dan...@us...> - 2007-08-15 10:48:31
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Revision: 126
http://obi.svn.sourceforge.net/obi/?rev=126&view=rev
Author: daniel_schober
Date: 2007-08-15 03:48:27 -0700 (Wed, 15 Aug 2007)
Log Message:
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The corresponding Call Notes: InstrumentMinutes14August2007
Participants: Ryan Brinkmann, Allyson Lister, Daniel Schober
Checking marked classes: ?column_chromatography_solvent goes to Biomaterial
?collection_tube is it cardinal part of fluidic system? Move to Labware?
flow_cell ? Make name more explicit is it a chamber as its subclasses imply?
?jet_in_air_flow_chamber is a Flow cell? (apply naming convention: Dont use ellipse or apocope, be explicit. 'Flow cell' consists of qualifier terms and omits the head noun. Ryan: What is a flow cell? better 'flow cell compartment'?
?interrogation_point not an object, more a location or spatial entity
?sample_fluid, ?sheath_fluid DS: Is a fluid an instrument? Or even part of an instrument ? Its a biomaterial.
same with ?sheath_propellent
?flow_cytometer: DS: Is this class justified? (has currently only one subclass), ask Ryan and Function Branch for differrentiae...
Added a cytometer class and image cytometer.
?liquid_handler more an inferred thing? DS: Is this class justified? Its a unnamed class. If so, put a fluidic_system and the fluidic_subsystem as subclasses. TW: This is required by MO. FG & DS: Capture as function. All: Needs to be reviewed, according to query use case. If we keep it its kept as unnamed owl class. The liquid handling class remains but as an undefined class with are unlikely to have children. It is expected that the reasoner would classifiy appropriate classes under this class that meet the have the liquid_handling function relation.
liquid_chromatography_instrument (removed comment and questiobnmark.
Checked for obo foundry naming convention: as under http://obofoundry.org/wiki/index.php/Naming Cleared some Labware Plurals...
Discussed deadlines and implications for our branch.
Discussed Subsystem and Part_of issues e.g. optical_subsystem
Modified Paths:
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branchDevelopment/trunk/InstrumentAndPart.owl
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From: <dan...@us...> - 2007-08-17 14:27:02
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Revision: 132
http://obi.svn.sourceforge.net/obi/?rev=132&view=rev
Author: daniel_schober
Date: 2007-08-17 07:27:01 -0700 (Fri, 17 Aug 2007)
Log Message:
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Branch was checked to conform to naming conventions.
Some class positions were altered and some orthographic glitches rectified.
Here the complete change track:
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
Modified Paths:
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branchDevelopment/trunk/InstrumentAndPart.owl
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From: <mco...@us...> - 2007-10-16 16:04:15
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Revision: 163
http://obi.svn.sourceforge.net/obi/?rev=163&view=rev
Author: mcourtot
Date: 2007-10-16 09:04:18 -0700 (Tue, 16 Oct 2007)
Log Message:
-----------
add note for instrument
Modified Paths:
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branchDevelopment/trunk/InstrumentAndPart.owl
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From: <mco...@us...> - 2007-10-16 16:12:42
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Revision: 164
http://obi.svn.sourceforge.net/obi/?rev=164&view=rev
Author: mcourtot
Date: 2007-10-16 09:12:43 -0700 (Tue, 16 Oct 2007)
Log Message:
-----------
added editor note
Modified Paths:
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branchDevelopment/trunk/InstrumentAndPart.owl
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From: <mco...@us...> - 2007-10-24 13:55:00
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Revision: 172
http://obi.svn.sourceforge.net/obi/?rev=172&view=rev
Author: mcourtot
Date: 2007-10-24 06:55:01 -0700 (Wed, 24 Oct 2007)
Log Message:
-----------
added required metadata
Modified Paths:
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branchDevelopment/trunk/InstrumentAndPart.owl
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From: <dan...@us...> - 2007-11-06 17:27:49
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Revision: 177
http://obi.svn.sourceforge.net/obi/?rev=177&view=rev
Author: daniel_schober
Date: 2007-11-06 09:27:53 -0800 (Tue, 06 Nov 2007)
Log Message:
-----------
updated questionable classes and removed questionmarks.
Modified Paths:
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branchDevelopment/trunk/InstrumentAndPart.owl
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From: <fgi...@us...> - 2007-12-05 15:22:43
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Revision: 190
http://obi.svn.sourceforge.net/obi/?rev=190&view=rev
Author: fgibson_sf
Date: 2007-12-05 07:21:51 -0800 (Wed, 05 Dec 2007)
Log Message:
-----------
Reviewed the branch and the annotation properties for
definition, example of use, definition_editor and definition_citation for the following terms:
-device
-instrument
-labware
-gamma counter
-incubator
-light source (normalised definition)
-arc lamp (normalised definition)
-laser (normalised definition)
-helium neon ion laser (normalised definition)
-mixed argon krypton gas laser (normalised definition)
-metal vapor laser (normalised definition)
-helium cadmium ion laser (normalised definition)
-optical filter (normalised definition)
-band pass filter (normalised definition)
-dichroic filter (normalised definition)
-dichroic mirror (normalised definition)
-long pass filter (normalised definition)
-short pass filter (normalised definition)
-DNA sequencer (normalised definition)
-array scanner (normalised definition)
-arrayer (normalised definition)
-mass spectrometry instrument changed to mass spectrometer
Modified Paths:
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branchDevelopment/trunk/InstrumentAndPart.owl
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