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- ...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
- #REDIRECT [[Data Jamboree 2/Notes]]35 bytes (4 words) - 03:48, 7 October 2008
- 26 bytes (2 words) - 00:44, 9 January 2009
- ...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
File:Phenoscape Data Roundup.pdf (110 KB) - 17:35, 8 February 2009- ...ma of this data repository and outlines the methods to load and query this data repository. == Data Repository ==18 KB (2,662 words) - 21:46, 14 December 2009
- #REDIRECT [[Conceptual Model of Data Warehouse]] '''Description of the data warehouse conceptual schema '''108 bytes (14 words) - 13:48, 21 August 2009
- '''File formats (for data downloads)'''263 bytes (36 words) - 19:55, 19 March 2012
- This page documents data integrity checks that would be useful to implement in a testing framework r = Data =862 bytes (119 words) - 21:41, 17 November 2011
- #REDIRECT [[Phenoscape data policy]]36 bytes (4 words) - 23:10, 29 October 2014
Page text matches
- ...for evolutionary biology, designed to help biologists analyze comparative data about organisms." Mesquite is written in Java and supports extension via t764 bytes (99 words) - 23:51, 10 January 2009
- WG:PI Meeting 5Jun07
- ...nder a Creative Commons Attribution 3.0 Unported license (see [[Phenoscape data policy]]) ...Phenex and available on GitHub at https://github.com/phenoscape/phenoscape-data.3 KB (364 words) - 01:17, 26 March 2019
- ...Notes#Taxon Concepts | Summary of a discussion of TTO issues at the second data jamboree (September 2008)]] Here is a preliminary taxonomy ontology, using data from a somewhat dated CoF dump. The taxa represented here are mentioned in29 KB (4,235 words) - 17:01, 31 August 2010
- [DONE] [nvarchar] (1) -- Once used to track data entry status; no longer used.7 KB (879 words) - 23:45, 10 January 2009
- WG:Call 31Aug07
- ...s to be productively and efficiently used by curators -- March 2008 (first Data Jamboree)=== * '''[complete]''' Initial Phenote configuration for PhenoScape data model.4 KB (512 words) - 19:26, 11 October 2011
- ...tions|driving biological research questions]] that take advantage of these data to push the limits of what is currently possible, and to identify what info8 KB (1,031 words) - 19:29, 11 January 2009
- ...web-based interfaces to ensure that the system we are developing, and the data that we are collecting, will allow the research community to obtain answers ...t developmental and morphological phenotypes, single-gene mutant phenotype data from zebrafish would allow a detailed analysis of this issue for any evolut2 KB (332 words) - 05:26, 10 September 2008
- - structure of data would be fluid PM - data is representation of current knowledge - can change over time5 KB (829 words) - 20:03, 18 January 2008
- * collect imaging data, have sparser data on electrophysiology time series * kinds of data collected: expression imaging, histological sections, videos of behavior7 KB (1,020 words) - 20:03, 18 January 2008
- ...d ways for doing character reconstruction - user will probably want to get data and run themselves3 KB (480 words) - 20:04, 18 January 2008
- -have sets of data mapped on tree – for example , all in situs done for a particular gene… ...ave been done at all for species of interest; see which species have that data, download all the images.2 KB (308 words) - 20:04, 18 January 2008
- * need environmental, ecological, and geographical data2 KB (289 words) - 20:04, 18 January 2008
- ===Additional data types and query constraints=== [[Image:Day2-dataintegration.whiteboard.JPG|thumb|right|384px|Data interrelationships]]1 KB (125 words) - 20:05, 18 January 2008
- [[Image:Day2-dataintegration.whiteboard.JPG|thumb|right|384px|Data interrelationships]] * Other data types or dimensions we haven't looked at3 KB (470 words) - 20:05, 18 January 2008
- ** how to link these two through, for example, a data repository3 KB (453 words) - 20:03, 18 January 2008
- HL – might get data on a mutant that indicate that the red dot changed position PM – would be nice to have a representation that let you see data in two different ways7 KB (1,183 words) - 20:04, 18 January 2008
- ...ets of their interest that took advantage and promoted reuse of the KB’s data and services. ...oevolutionary patterns. A similarly rich set of tools, such as ontologies, data annotation models, and machine reasoners, have also recently been introduce18 KB (2,453 words) - 00:15, 10 December 2019
- * Data curation: Dahdul et al. (2018), Dahdul et al. (2015), Cui et al. (2015), Ar * Data modeling, reasoning & ontologies: Mabee et al. (2020), Manda et al. (2016)52 KB (6,895 words) - 22:42, 17 November 2023
- ...ode phenotypic data from an existing publication into the EQ format. This data consists of descriptions of character state values for corresponding specie ===Data Model===7 KB (1,124 words) - 23:41, 10 January 2009
- ...otations to specimens within publications has been at issue. Our existing data model held all phenotype annotations at the level of particular specimens. Our discussion at the Biocuration meeting led to a new data model in which all phenotype annotations are expressed as properties of spe2 KB (393 words) - 21:55, 22 November 2008
- WG:PhenoScape monthly conference call
- ...logical, spatial, and other requisite domain knowledge, the KB links these data to phenotypes reported in genetic perturbation studies for pertinent model For query answering the KB uses machine reasoning to match data by its semantics. The API also gives access to other machine reasoning-base1 KB (186 words) - 19:16, 26 September 2017
- WG:PhenoScape monthly conference call/2015
- In the process of annotating data files, curators may encounter terms in the data that have not yet been added to an appropriate ontology. Requesting a new o ...enoscape ontology editors can review the requested terms, independently of data annotation work. After adding a term to an appropriate ontology, or decidin3 KB (457 words) - 18:07, 13 November 2015
- ..., and software infrastructure and services, bringing together evolutionary data matrices annotated by Phenoscape curators, model organism phenotype and gen ==Data sources==9 KB (1,386 words) - 13:53, 20 March 2014
- The [http://www.evolutionaryontology.org/cdao Comparative Data Analysis Ontology] (CDAO) includes classes and properties for modeling phyl2 KB (350 words) - 20:31, 8 July 2013
- ...expressions are not equivalent but describe different aspects of the same data model.6 KB (853 words) - 20:39, 18 October 2013
- WG:PhenoScape monthly conference call/2010
- ...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
