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From phenoscape

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  • ...the ontology-specific functions enumerated below, and the Phenoscape KB [[Data Services]] implement a much richer set of phenotype annotation services tha ...h as EQ editors that heavily rely on such a service to plug into different data providers, local or remote, at their choice.
    7 KB (1,119 words) - 20:41, 20 September 2011
  • ==Description of data model== The data warehouse has been designed with the intent of maximizing the efficiency of
    2 KB (264 words) - 15:30, 8 September 2009
  • #REDIRECT [[Ontology Data Service API]]
    39 bytes (5 words) - 15:10, 18 April 2007
  • ...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
  • ...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 discussion
    2 KB (267 words) - 23:29, 17 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  • '''PhenoscapeKB Data Policy''' ...original paper (or, in some cases, unpublished manuscript) from which the data were derived, as well as a citation of the following form: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
  • #REDIRECT [[Data Jamboree 1/Agenda]]
    36 bytes (4 words) - 02:36, 12 April 2008
  • 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
  • ...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 interface
    8 KB (1,022 words) - 20:08, 1 March 2011
  • #REDIRECT [[Data Jamboree 2/Agenda]]
    36 bytes (4 words) - 01:48, 27 July 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
  • ** Empty current data from DB '''Done''' ** Continue DB data loading work '''Done'''
    1 KB (177 words) - 18:24, 26 September 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
  • * ability to prune species with no data (values) for export * Summarizing data per publication
    19 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
  • #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 retrieved
    46 KB (4,930 words) - 19:11, 29 June 2016
  • ...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

  • * [[Phenoscape data policy]]
    151 bytes (16 words) - 23:41, 10 January 2009
  • * [http://www.berkeleybop.org/obd/ Open Biomedical Data (OBD) data model, API, and other downloads]
    4 KB (476 words) - 19:39, 24 May 2018
  • ...igured to load user-selected ontologies, and in this way can be adapted to data curation in different taxonomic groups. ===Phenoscape data repository===
    6 KB (808 words) - 22:14, 10 November 2012
  • Phenotype data for model organisms are imported into the Phenoscape KB for mouse (MGI), hu ...nks to their pages). Taxonomic synonyms are particularly useful as aids to data curation, but common names can assist users in browsing the website. Taxono
    14 KB (2,022 words) - 17:42, 17 July 2018
  • ...ations. When it is ready, we plan to integrate it with [[Phenex]], so that data curators can take advantage of natural-language processing to accelerate th
    1 KB (177 words) - 20:34, 26 March 2013
  • ...g limitations in comparative studies of trait evolution: recombining trait data, modeling trait evolution, and generating testable hypotheses for the drive
    3 KB (426 words) - 22:31, 13 December 2019
  • ...the ontology-specific functions enumerated below, and the Phenoscape KB [[Data Services]] implement a much richer set of phenotype annotation services tha ...h as EQ editors that heavily rely on such a service to plug into different data providers, local or remote, at their choice.
    7 KB (1,119 words) - 20:41, 20 September 2011
  • ...be gray. By clicking on the column within the row you will be able to add data. #Go to:''' Data Set''' panel, go to Publication, and type in the author(s) and year for the
    8 KB (1,303 words) - 20:56, 26 November 2012
  • #REDIRECT [[Ontology Data Service API]]
    39 bytes (5 words) - 23:56, 10 January 2009
  • ...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==
    8 KB (1,279 words) - 17:54, 5 November 2008
  • ==Description of data model== The data warehouse has been designed with the intent of maximizing the efficiency of
    2 KB (264 words) - 15:30, 8 September 2009
  • ...group will tackle the logistics of developing such a database, from basic data entry curation through programming, beginning with a prototype.
    4 KB (634 words) - 23:47, 10 January 2009
  • ...other. Furthermore, metrics such as semantic similarity can provide useful data that can be integrated into many steps in a phylogenetic comparative analys
    5 KB (740 words) - 21:57, 16 December 2019
  • ...s, with no place to reference an independent character. So you may have a data set like this: ...or", and 1 value for "pectoral fin color". But nowhere in the existing EQ data formats is the character stored. We have to infer it from the PATO hierarc
    7 KB (1,089 words) - 23:42, 10 January 2009
  • Here is sample data in the default configuration:
    935 bytes (135 words) - 23:57, 10 January 2009
  • ...for evolutionary biology, designed to help biologists analyze comparative data about organisms." Mesquite is written in Java and supports extension via t
    764 bytes (99 words) - 23:51, 10 January 2009
  • ...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 in
    29 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
  • ...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 info
    8 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 evolut
    2 KB (332 words) - 05:26, 10 September 2008
  • - structure of data would be fluid PM - data is representation of current knowledge - can change over time
    5 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 behavior
    7 KB (1,020 words) - 20:03, 18 January 2008
  • ...d ways for doing character reconstruction - user will probably want to get data and run themselves
    3 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 data
    2 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 at
    3 KB (470 words) - 20:05, 18 January 2008
  • ** how to link these two through, for example, a data repository
    3 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 ways
    7 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 introduce
    18 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 spe
    2 KB (393 words) - 21:55, 22 November 2008
  • ...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-base
    1 KB (186 words) - 19:16, 26 September 2017
  • 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 decidin
    3 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 phyl
    2 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
  • ...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/Brea
    10 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 discussion
    2 KB (267 words) - 23:29, 17 April 2008
  • * 1:00 pm Working session on individual data * 3:30 pm Working session on individual data and group discussion
    3 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
  • ...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 componen
    17 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.or
    4 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 unt
    4 KB (615 words) - 20:04, 9 July 2008

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