Activity for OBI
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Chris Stoeckert posted a comment on ticket #826
We've moved the issue tracker to GitHub! Please see https://github.com/obi-ontology/obi/issues/806 Thanks, Chris
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Jason Hilton posted a comment on ticket #826
Apologies. Please try this document for microRNA counts... https://www.nanostring.com/application/files/9614/8964/8051/MAN-C0009-05_nCounter_miRNA_Expression_Assay.pdf
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James A. Overton posted a comment on ticket #831
Moved to GitHub as https://github.com/obi-ontology/obi/issues/817 I'm going to close...
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cloud condensation nucleus counter
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MOVE TO GitHub!!
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Yes, we are happy to put this in OBI. Note we are moving to Github for issue trackers...
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anna maria masci posted a comment on ticket #832
THIS TERM BELONG TO OBIB SO PLEASE CANCEL THE REQUEST
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specimen integrity
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PL Buttigieg created ticket #831
cloud condensation nucleus counter
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Rebecca Tauber created ticket #830
NTRs for ECO-OBI collaboration
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Rob Nash posted a comment on ticket #823
Thanks again! Rob
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Thanks James!
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Add sheet with 14 new terms
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This empty annotation was removed in commit 4092. Sorry for the delay.
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empty/null value for a property in OBI
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Remove empty annotation
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This term was added as OBI_0002132 in commit 4091, and will be included in the next...
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New Term Request: Pulse SILAC
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Add OBI_0002132
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New Term Requests: assays
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Hi Rob, I apologize for dropping the ball on this. The terms have been added to OBI...
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Adopt four CHMO terms into OBI
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Hi Jie, Much appreciated! Thanks, Rob
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jzheng posted a comment on ticket #794
Hi Rob, We discussed the tracker on 2017-02-20 OBI dev call. James will add the terms....
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bjoernpeters posted a comment on ticket #823
Reworded definition: An assay that detects differences in protein abundance using...
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New Term Request - Illumina HiSeq X Ten
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Added to OBI as part of #826.
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Added the sequencer and bead chip terms to OBI.
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added sequencer and BeadChip terms requested in...
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Need to standardize the definitions (see below). Will address the 10HiSeqX and note...
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Thanks so much Jie. I was preparing for a future project which is now just around...
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Hi Rob, We will discuss the trackers (794, and 823) you submitted on OBI dev call...
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Hi, Were these terms ever added? I cannot seem to see them in OBI. Cheers, Rob
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Hi, Noticed that this term may not yet have been added? Please let me know if I missed...
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NTRs (requested by project ENCODE)
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empty/null value for a property in OBI
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Mathias created ticket #829
add new class to represent clinical assessments (handedness, tumor grading)
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Edit 'cell specimen' and add 'single cell speci...
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handle single cell specimen
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Comments from Bjoern: The grain/part/component stuff is a mess. The grain/part/component...
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has part is a transitive property cannot be used to set cardinality constraint. Need...
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Discussed on obi call Jan 23, 2017 Will edit cell specimen and add single cell specimen...
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handle single cell specimen
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Sirarat Sarntivijai posted a comment on ticket #828
Thanks so much Jie! To add to that, could I also please request a new term 'single...
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handle single cell specimen
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empty/null value for a property in OBI
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NTR: stained fixed slide specimens
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These have been added to OBI
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added stained slide specimens as per tracker #825
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added stained slide specimens as per tracker #825
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added stained slide specimens as per tracker #825
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NTRs (requested by project ENCODE)
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discussed on 12/12 call suggestion is H&E-stained, IHC-stained
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NTR: stained fixed slide specimens
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Classify enzymes
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Came up again on Nov 21, 2016 call going over specified inputs to assays. Agree that...
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Add 'geometric mean calculation'
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regarding value specifications
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assay term request
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Change the output of assay: from 'information content entity' to 'data item'
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New Term Requests: assays
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New Terminologies for OBI (Yale Med School)
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Specified input issue for chromosome organization assay by FISH
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New Term Request: Pulse SILAC
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New Term Request: Pulse SILAC
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New Term Request: Pulse SILAC
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Discussed on 2016-10-24 OBI call. Not so clear how to improve it. It needs further...
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qualities without matching processes
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Discussed on 2016-10-24 OBI call. We don't require that quality always associate...
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manufacturing defined class
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Discussed on 2016-10-24 OBI call. There is no issue anymore. Now device is associate...
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grouping processes - assays vs process - granularity issue
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Discussed on 2016-10-24 OBI call. The issued addressed in assay harmonization discussion...
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specimen creation
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Discussed on 2016-10-24 OBI call. We renamed specimen creation to specimen collection...
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Discussed on 2016-10-24 OBI call. We agreed with the comments on the term 'waiting'....
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Discussed on 2016-10-24 OBI call. The issue is not relevant any more.
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Cellular_component
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Should scattered_molecular_aggregate be a defined class?
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Discussed on 2016-10-24 OBI call. No driving use cases so far. Nothing inferred under...
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action specification
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These IAO terms were updated during the Core Review in 2012. The problems mentioned...
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Call 10/17: The assays now exist in OBI. closing this item.
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flow cytometry terms
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Ticket 155 was related to this (raw vs. processed data). We might want to be able...
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Ticket 810 deals with this.
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Raw Data vs Processed data
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10/17, call, closing this ticket. The 'original' data from a given assay is the specified...
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comments from Robert H.
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Committing OBI release 2016-10-11
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Include a few more annotation properties
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Include more annotation properties in core
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Remove OBI_0002117 synonym 'WES'
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remove hyphen from in-situ hybridization
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Fixed in commit r4080.
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Remove hyphen from 'in-situ', fixes #821
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assay harmonization - inputs of assay
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assay harmonization - device
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assay harmonization - outputs of assay
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assay harmonization - objective
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