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• 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
• Queries and Query Execution Plans
  ...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 bottlen
  3 KB (429 words) - 20:30, 21 January 2009
• Logic and Reasoning Challenges
  ...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 relati
  18 KB (2,610 words) - 17:18, 22 February 2010
• Phenoscape data loader
  ...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
• Data Services
  {{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
• Queries
  ...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 the
  3 KB (409 words) - 18:07, 21 August 2009
• ORB term request prototype
  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
• Queries for Phenoscape UI demo'ed at SICB, Boston in Jan 2009
  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
• Synchronization Tool
  ====Conflicting Data====
  3 KB (526 words) - 22:05, 23 January 2009
• OBD Java API
  This page contains documentation of the data services module of the Phenoscape project, and supplements the [[http://www
  274 bytes (41 words) - 23:20, 31 July 2009
• OpenURL
  ...adata about publications, however to describe access requests, it contains data for:
  2 KB (385 words) - 23:39, 18 February 2009
• Neglected items
  ...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
• Query strategy performance
  ...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
• Creating Tree Files
  ...tml Mesquite]. You might begin with an existing nexus file containing the data matrix for the publication, or create a new nexus file containing a list of # Open the nexus file in Mesquite. You should see the data matrix with the taxon list in the left-hand column.
  2 KB (316 words) - 21:19, 26 November 2012
• Current queries
  This page documents the queries implemented to retrieve data for the Anatomy Web Services module of the Phenoscape project, which was de ...the client side, which is a very expensive process in terms of time. Some data structures like lookup tables for Attributes and Values have been implement
  4 KB (540 words) - 19:52, 20 January 2009
• Query execution speed-up: The investigation
  ...ractShard and the OBDSQLShard contain method definitions that can retrieve data from the repositories by executing SQL or more XML based query formats. For The Phenoscape data is stored in a database that is managed through the PostgreSQL RDBMS (Versi
  2 KB (375 words) - 15:02, 21 August 2009
• SummerTraining2009
  ...ata. Opportunities are available to work as part of the Phenoscape team on data curation or open source software/database development. Participants would
  2 KB (323 words) - 02:51, 2 February 2009
• Student Instructions
  ...sed in a shared [http://www.dropbox.com DropBox] folder (named 'Phenoscape-data'). Please contact Wasila or Paula for access. <nowiki>https://webdav.nescent.org/phenoscape-data</nowiki>
  2 KB (253 words) - 20:06, 29 November 2012
• Entities with taxonomic context
  ...effect on data curators - the interface would be the same in Phenex. The data would be modeled in this way on its way into OBD. So, there would be no ne
  4 KB (552 words) - 14:26, 30 March 2009
• Phenoscape data repository
  ...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
• ASIH09 workshop
  ...es of how these ontologies are being used to provide new ways of exploring data within morphological and phenotypic databases. Talks in the morning will be As biology has become increasingly data-rich, the reliance on databases and
  14 KB (1,979 words) - 14:02, 13 August 2009
• Phenotype Ontology Coordination Workshop
  ...ttp://www.nsf.gov/pubs/2007/nsf07565/nsf07565.htm INTEROP (Community-based Data Interoperability Networks)] application to NSF that we would submit in July * 2. What are key obstacles to data exchange and data integration?
  10 KB (1,285 words) - 02:21, 21 February 2011
• 2009 Grant Renewal Workshop
  ...e between different concepts of homology, extending the systematics legacy data transformation to all vertebrates, and laboratory case-studies for followin ...ary skeletal phenotypes associated with skeletal phenotypes and associated data from MODs.
  7 KB (857 words) - 22:19, 10 February 2012
• Phenoscape Grant Renewal Workshop/Notes
  ** MGI, Xenbase, and ZFIN all have links from their phenotype data to OMIM ...te testable hypotheses; how exactly do those queries rely on developmental data?
  16 KB (2,313 words) - 17:34, 22 May 2009
• Knowledgebase mockups
  ==Grouping data by using an ontology tree view== Possible further enhancement to page capabilities - redisplay data on a quality tree. The included results would be somewhat different.
  6 KB (946 words) - 19:58, 19 January 2010
• Conceptual schema of the Phenoscape data warehouse
  #REDIRECT [[Conceptual Model of Data Warehouse]] '''Description of the data warehouse conceptual schema '''
  108 bytes (14 words) - 13:48, 21 August 2009
• Acknowledgments
  ...tributed to Phenoscape ontology development, data curation, workshops, and data entry: ===Curators (Data Annotation)===
  16 KB (2,112 words) - 23:44, 16 December 2019
• Author Guide
  ...h with ostariophysan fishes, beginning with the papers that have published data matrices. Learn more about the project and the ontologies used by Phenoscap The morphological variation reported in systematic character data is documented in phenotype statements recorded in Entity-Quality syntax. '
  4 KB (580 words) - 21:32, 15 June 2009
• Knowledgebase mockups (Nov 2009)
  * Tree page, source data box: will need link to Pub page 3, below (case # 1337) ...ted smaller source character text under each publication to indicate which data caused association of that publication with ontological term on previous pa
  7 KB (994 words) - 18:49, 21 January 2010
• Terminology
  ...xon) Name: The taxon name used in a publication from which we have curated data. [[Category:Data]]
  4 KB (599 words) - 16:19, 4 June 2013
• Knowledgebase/Ideas for the future
  ...bservation for example). So how could users add comments on the registered data? How could they discuss, make decisions on statements? Would it be feasible
  586 bytes (90 words) - 21:21, 2 December 2009

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