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- ...to enable synthetic research that takes full advantage of the accumulated data in each of these fields. We hoped to identify driving biological questions ...ife history, adaptation, and evolutionary time with phenotypic and genetic data to elucidate mechanisms of phenotypic change [[Needs Analysis Workshop/Brea10 KB (1,445 words) - 05:23, 10 September 2008
- ...olution to Genomics Using Phenotype Ontologies:'''<br/>'''First Morphology Data Jamboree'''</big><br/><br/>A workshop hosted by the National Evolutionary S ...ct personnel to work one-on-one on entering published systematic character data.9 KB (1,267 words) - 19:28, 11 January 2009
- * 1:00 pm Working session on individual data * 3:30 pm Working session on individual data and group discussion2 KB (267 words) - 23:29, 17 April 2008
- Index of pages tagged with category 'Data Jamboree'.0 members (0 subcategories, 0 files) - 02:49, 8 February 2008
- Index of pages tagged with category 'Data Jamboree 1'.5 members (0 subcategories, 0 files) - 21:58, 22 November 2008
- * 1:00 pm Working session on individual data * 3:30 pm Working session on individual data and group discussion3 KB (452 words) - 19:43, 16 April 2008
- '''PhenoscapeKB Data Policy''' ...original paper (or, in some cases, unpublished manuscript) from which the data were derived, as well as a citation of the following form:1 KB (174 words) - 13:39, 26 March 2019
- WG:Notes from participants
- WG:All-Hands Meeting 21Apr08
- ...take care of appending this for you.'' The Phenoscape configuration saves data for a project in 3 files; for this reason it is a good idea to create a sep The editor component displays a detailed data entry interface for the currently selected row in one of the table componen17 KB (2,828 words) - 20:06, 1 March 2011
- An annotation experiment was conducted on day 2 of the April 2008 Data Jamboree in order to assess curation consistency among the four trained par ...e following exercise, we would like to assess annotation consistency among data jamboree participants working independently on a common set of characters.15 KB (1,736 words) - 18:18, 10 April 2013
- The first Phenoscape [[Data Jamboree 1|data jamboree]] revealed that our curation workflow implemented in Phenote could ...ter states. As such, the curator will need to deal with far fewer rows of data when working in Phenote, as compared to simultaneous taxon annotation.13 KB (2,129 words) - 13:47, 9 September 2008
- ...the [http://bioportal.bioontology.org/visualize/38362 NCBO BioPortal] and data annotated using TAO terms can be queried using the [http://kb.phenoscape.or4 KB (661 words) - 01:37, 15 August 2012
- ...ckup your file to the "Character-EQ lists (phenote+) folder" on phenoscape-data file share. *You can enter data directly in the Annotation Table by double or triple clicking on a cell unt4 KB (615 words) - 20:04, 9 July 2008
- You can sort the data by clicking on any column header. Sort the "Taxon Comments" column to view ...te those that were used in the matrix. To find taxa associated with matrix data, look at: 1) the '''Matrix Taxon''' column in the Taxa Panel, which will co5 KB (759 words) - 21:14, 26 November 2012
- ...lution to Genomics Using Phenotype Ontologies:'''<br/>'''Second Morphology Data Jamboree'''</big><br/><br/>A workshop hosted by the University of South Dak # Character data entry by experts; introduce new curators to Phenote and data entry; test/enhance curation consistency; further refine curation interface8 KB (1,022 words) - 20:08, 1 March 2011
- Index of pages tagged with category 'Data Jamboree 2'.7 members (0 subcategories, 0 files) - 21:58, 22 November 2008
- Agenda for the 2nd Phenoscape Data Jamboree and Project Meeting, held in South Dakota: * 9:45 am: Phenoscape data policy (Todd Vision)3 KB (367 words) - 03:57, 7 October 2008
- ...ble reports of query results (e.g. candidate genes; comparative phenotypic data)" as a priority --[[User:Pmabee@usd.edu|Pmabee@usd.edu]] 18:15, 18 August 2 ...ven character values (or ambiguity) using, e.g. parsimony. The phenotypic data matrix is shown at the tips.14 KB (2,054 words) - 16:38, 26 September 2008
- ...to large-scale computation so that they can be subjected to computational data integration and knowledge discovery techniques in ways similarly powerful a ...enotypes for vertebrate fin and limb characters with genetic and phenotype data from three vertebrate model organisms: [http://zfin.org zebrafish] (''Danio7 KB (945 words) - 20:11, 13 December 2019
- ...lt of this pipeline is a unified OWL dataset containing the ontologies and data. The result is loaded as RDF into a [[Bigdata|Blazegraph]] triplestore. ...ion. In doing so the inputs are, as far as possible, converted to a shared data model. EQ annotations are converted to a specific semantic representation.11 KB (1,489 words) - 18:14, 27 July 2015
- * Began mapping of Phenex data model to OBD model. This is currently implemented in <code>org.phenoscape. .... However, this presents complications for adding or modifying data for a data set already in OBD.7 KB (1,072 words) - 02:38, 26 August 2008
- ** Empty current data from DB '''Done''' ** Continue DB data loading work '''Done'''1 KB (177 words) - 18:24, 26 September 2008
- database from scratch. If all primary data is in cvs/svn/ftp we lose3 KB (505 words) - 02:31, 25 August 2008
- ***Revise same (Group annotation exercise) from data jamboree 1 ...icipants regarding their three assigned publications for annotation at the data jamboree -3 KB (392 words) - 17:43, 24 September 2008
- WG:All-Hands Meeting 30Sep08
- * ability to prune species with no data (values) for export * Summarizing data per publication19 KB (2,935 words) - 15:05, 14 October 2008
- ...to five curators on the third day of the [[Data_Jamboree_2/Agenda | second data jamboree]]. The goals of the experiment were to assess curation consistency Only one of the five curators had experience using Phenex prior to the data roundup. Training for all curators consisted of:7 KB (996 words) - 14:46, 8 October 2008
- * Could use OLS, but makes more sense to retrieve exact data we're working off of in the database ...summary counts be returned in? These are then used to navigate to further data services.2 KB (301 words) - 03:11, 23 October 2008
- * '''[Ongoing]''' Investigate and begin documenting additional data service needs required by interface * '''[Ongoing]''' Document data retrieval web service specifications5 KB (764 words) - 19:27, 11 October 2011
- ...e still under development, Phenex is ready for use and enables our ongoing data curation activities. ===Data services built on OBD===2 KB (256 words) - 23:48, 10 January 2009
- ** Mockup interface using dummy data within web application - request group feedback ** Possible live demo depending on data service performance progress6 KB (783 words) - 22:51, 9 January 2014
- * Implement improved query methods to speed up execution of anatomy data services * Automate data loader module2 KB (274 words) - 19:25, 11 October 2011
- ...inally reasons with (as in infers implicit knowledge from) the downloaded data. ==OBD Data Model Entities==11 KB (1,531 words) - 16:06, 8 January 2009
- ...is an excerpt from such a Problem Log created during the execution of the Data Loader. The problematic, incomplete records are grouped under the name of t3 KB (365 words) - 23:59, 10 January 2009
- Mockup drawings created at the Phenoscape Data Roundup in September 2008. These are intended to stimulate discussion and [[Category:Data Jamboree 2]]1 KB (185 words) - 19:58, 19 January 2010
- ...s the queries that have been (or are to be) implemented for the Phenoscape data services, in addition to the execution details of each queries on the Postg ...onal, but their execution was very slow in terms of time. As a result, the data retrieval strategy used in the SICB prototype is being examined for bottlen3 KB (429 words) - 20:30, 21 January 2009
- WG:All-Hands Meeting 5Jan09
- ...a, adding top-down inferencing may cause widespread inconsistencies in the data if unchecked. ...between taxa and phenotypes, would cause incorrect inferencing and loss of data integrity. The easiest way to address this issue is to use different relati18 KB (2,610 words) - 17:18, 22 February 2010
- ...ation server at NESCent and can be found at /usr/local/projects/phenoscape-data-loader ==The Phenoscape data loader - A step by step review==3 KB (515 words) - 16:05, 29 October 2009
- {{StatusBox|This page documents data services for version 1 of the Phenoscape KB, available as a legacy resource This page details the data services that query the Phenoscape OBD database and transfer the retrieved46 KB (4,930 words) - 19:11, 29 June 2016
- ...ection describes the queries that have been implemented for the Phenoscape data services, in addition to the execution details of each queries on the Postg ...d and an execution plan is drawn up by the PostgreSQL DBMS to retrieve the data as efficiently as possible in terms of time and memory utilization. In the3 KB (409 words) - 18:07, 21 August 2009
- WG:All-Hands Meeting 9Sept09
- The vision of this project is to develop an application that will allow data curators to use new ontology terms without creating a workflow bottleneck. ...provenance and community discussion, enable temporary terms to be used in data annotation, and update temporary terms once a request has been resolved.30 KB (4,747 words) - 13:13, 3 October 2010
- This page documents the queries implemented to retrieve data for the Anatomy Web Services module of the Phenoscape project, which was de ...eries Q2 and Q3 are avoided. Coupled with connection, query execution, and data transfer times, this leads to significant time savings.3 KB (531 words) - 20:12, 28 January 2009
- ====Conflicting Data====3 KB (526 words) - 22:05, 23 January 2009
- This page contains documentation of the data services module of the Phenoscape project, and supplements the [[http://www274 bytes (41 words) - 23:20, 31 July 2009
- ...adata about publications, however to describe access requests, it contains data for:2 KB (385 words) - 23:39, 18 February 2009
- ...gy (such as "millimeters"). These values are not imported into OBD by the data loader. Data matrices sometimes use the NEXUS format for specifying polymorphic states.3 KB (488 words) - 13:37, 30 April 2009
- ...e the execution times. This page discusses the requirements of the various data access modules of the Phenoscape application to be demonstrated at the ASIH = Phenotype data summaries and details services =28 KB (4,482 words) - 16:37, 24 April 2009
