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  • Needs Analysis Workshop
    ...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
  • Driving Research Questions
    ...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
  • Needs Analysis Workshop/Breakout group 1
    - 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
  • Needs Analysis Workshop/Breakout group 2
    * 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
  • Needs Analysis Workshop/Correlation Breakout
    ...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
  • Needs Analysis Workshop/Phylogeny Breakout
    -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
  • Needs Analysis Workshop/Report-out Day1
    * need environmental, ecological, and geographical data
    2 KB (289 words) - 20:04, 18 January 2008
  • Needs Analysis Workshop/Prioritization
    ===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
  • Needs Analysis Workshop/Report-out Day2
    [[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
  • Needs Analysis Workshop/Chalk talks
    ** how to link these two through, for example, a data repository
    3 KB (453 words) - 20:03, 18 January 2008
  • Needs Analysis Workshop/Semantics Breakout
    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
  • Training and Workshops
    ...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
  • Publications and Posters
    * 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
  • EQ Editor requirements draft 1
    ...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
  • Hypodigm
    ...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
  • Knowledgebase
    ...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
  • Ontology Request Broker
    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
  • Phenoscape KB
    ..., 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
  • Individual-based taxonomy
    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
  • Absence Phenotypes in OWL
    ...expressions are not equivalent but describe different aspects of the same data model.
    6 KB (853 words) - 20:39, 18 October 2013
  • Needs Analysis Workshop/Summary
    ...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
  • Data Jamboree 1
    ...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
  • Data Jamboree 1/Agenda
    * 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
  • Jamboree 1/Agenda/Project Personnel
    * 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
  • Phenoscape data policy
    '''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
  • Phenote User Guide
    ...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
  • Data Jamboree 1/Annotation Experiment
    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
  • Matrix annotation workflow
    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
  • Teleost Anatomy Ontology
    ...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
  • Creating and Editing Character Lists
    ...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
  • Update Taxon Lists
    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 co
    5 KB (759 words) - 21:14, 26 November 2012
  • Data Jamboree 2
    ...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
  • Data Jamboree 2/Agenda
    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
  • Phenoscape use cases
    ...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
  • Ontology-enabled reasoning across phenotypes from evolution and model organisms
    ...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] (''Danio
    7 KB (945 words) - 20:11, 13 December 2019
  • KB build process
    ...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
  • BBOP OBD visit
    * 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
  • Data Jamboree 2/Prototype
    ** Empty current data from DB '''Done''' ** Continue DB data loading work '''Done'''
    1 KB (177 words) - 18:24, 26 September 2008
  • BBOP OBD visit/Chris notes
    database from scratch. If all primary data is in cvs/svn/ftp we lose
    3 KB (505 words) - 02:31, 25 August 2008
  • Data Jamboree 2/Preparation
    ***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
  • Data Jamboree 2/Notes
    * ability to prune species with no data (values) for export * Summarizing data per publication
    19 KB (2,935 words) - 15:05, 14 October 2008
  • Data Jamboree 2/Annotation Experiment
    ...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
  • Phenoscape web UI planning
    * 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
  • Roadmap for first iteration
    * '''[Ongoing]''' Investigate and begin documenting additional data service needs required by interface * '''[Ongoing]''' Document data retrieval web service specifications
    5 KB (764 words) - 19:27, 11 October 2011
  • Front end user interface tools
    ...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
  • Phenoscape web UI
    ** Mockup interface using dummy data within web application - request group feedback ** Possible live demo depending on data service performance progress
    6 KB (783 words) - 22:51, 9 January 2014
  • Database Roadmap
    * Implement improved query methods to speed up execution of anatomy data services * Automate data loader module
    2 KB (274 words) - 19:25, 11 October 2011
  • OBD API Documentation
    ...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
  • Problem Log Format
    ...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 t
    3 KB (365 words) - 23:59, 10 January 2009
  • Web UI mockups
    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

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