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• 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
• WG:All-Hands Meeting 30Apr09
• 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
• WG:All-Hands Meeting 25Jul09
• 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
• Anatomy Tree Display
  ...revision puts the ontology tree on the left as the primary browsing tool. Data for the selected term appears in the tabbed panels to the right. Possible further enhancement to page capabilities - redisplay data on a quality tree. The included results would be somewhat different.
  4 KB (563 words) - 16:24, 1 February 2010
• WG:All-Hands Meeting 20March10
• Transitive homology
  ...aking this strong assumption? We can explore this with existing phenoscape data.
  4 KB (642 words) - 02:29, 18 March 2010
• Change And Correlation
  === Slide 5: A tree with negative data and a detected change ===
  8 KB (1,097 words) - 20:55, 29 April 2010
• WG:All-Hands Meeting 11April10
• FMNH 2010 Workshop
  ...ating morphological data across studies and with genetic and developmental data. The user interface and tools are being designed to address the general ne
  3 KB (384 words) - 13:46, 4 May 2010
• Knowledgebase Reports
  ...It contains the latest public versions of all ontologies at the time the data were loaded, with the exception of PATO (it currently contains an [http://w * [http://kb.phenoscape.org/OBD-WS/timestamp/ Date on which these data were loaded]
  32 KB (4,884 words) - 15:32, 3 May 2012
• Reasoning over homology statements
  ...nd inferences laid out here have since been refined and adapted to an OWL2 data model. A manuscript describing competency questions, implementation, and as loss of efficiency due to storing redundant data).
  33 KB (5,448 words) - 22:33, 25 May 2018
• WG:All-Hands Meeting 18Oct
• EQ shortcuts (temporary)
  ...be used until better EQ entry interfaces are available in Phenex. The KB data loader will watch for and correctly interpret each of these. ...d X" qualities. While these qualities technically compare to "normal", the data loader will replace them with the correct quality.
  1 KB (163 words) - 02:07, 26 October 2010
• Knowledgebase:File formats (for data downloads)
  '''File formats (for data downloads)'''
  263 bytes (36 words) - 19:55, 19 March 2012
• Matching Phenotypes
  ...ut-off values for test statistic values of profile comparisons in the real data. For example
  16 KB (2,382 words) - 17:40, 16 July 2012
• WG:All-Hands Meeting 2011-11-11
• WG:All-Hands Meeting 2012-04-25
• Anatomy Ontology Conf calls
  ** "bulk" update grabs all chordate data; needs review by curator; would have list of species with invalid parents ...ning that every term in ZFA has a corresponding term in TAO; links to gene data.
  31 KB (4,773 words) - 20:15, 13 March 2012
• Collaborative Phenotype Annotation
  * import matrix data from file source (usually NEXUS) ** ''Supported. Can import character and state labels, matrix data from a NEXUS file. This is a one-time import before editing in MX.''
  12 KB (1,734 words) - 22:44, 18 September 2011
• Project Plan
  ...rature, will be integrated in the knowledgebase with genetic and phenotype data from three vertebrate model organisms: zebrafish (Danio rerio), African cl ...both extinct and extant vertebrates will be combined with mutant phenotype data from three vertebrate genetic models: zebrafish (Danio rerio), frog (Xenopu
  9 KB (1,278 words) - 17:11, 28 August 2012

• File:Phenoscape Project description refs.pdf ...lity to respond as any problems arise with integration of the evolutionary data and somewhat compromise our ability to rigorously evaluate the tools being (740 KB) - 10:10, 3 November 2011

• Term Definitions and References
  ...nitions facilitate the consistent use of a term in annotation of different data types by curators. We follow the convention that each term should have a te
  5 KB (707 words) - 16:42, 9 January 2012
• Semantics of phenotype annotations
  In Phenoscape data annotation, we typically model a phenotype as a class expression describing ...mes (an order), but would be the most appropriate choice for species-level data.
  3 KB (389 words) - 01:46, 29 August 2011
• Linking Evolution to Genomics Using Phenotype Ontologies
  ...o integrate developmental genetic and comparative morphological/anatomical data. ...database with its web-interface, together with the extended ontologies and data curation tools, will allow researchers to ask novel questions about the gen
  6 KB (922 words) - 18:05, 2 November 2011
• WebHints
  ...which meet the query criteria. These publications contain the evolutionary data matrices annotated by Phenoscape.
  7 KB (956 words) - 18:39, 19 March 2012
• KB-OWL
  This page describes the data model, data loading process, and query methods being developed for a new version of the ==Data model==
  4 KB (562 words) - 22:47, 9 January 2014
• Software
  ...quirements for scalability, reasoning expressivity, and support for linked data standards, we are developing a our Knowledgebase infrastructure using the R ...or semantically annotated character matrix files. This is the evolutionary data content for the Phenoscape KB. NeXML.
  9 KB (1,151 words) - 00:04, 10 December 2019
• KB data integrity checks
  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
• Phenoscape 1 Curated Publications
  ...omorph fishes: a total evidence approach using molecular and morphological data." Biochemical Systematics and Ecology 28: 319-350.
  11 KB (1,467 words) - 20:07, 11 November 2011
• WG:PhenoScape monthly conference call/2009
• To Edit is Divine
  ** Do we need a separate wiki page with a description of our data in EoL?
  2 KB (317 words) - 20:44, 19 April 2012
• Curation workflow
  ...ataset that a user should know. Generally, this includes notes on how the data was modified from the publication. For example, ....g., Information recorded here consists of modifications made to published data based on author communication, 10/12/2013).
  6 KB (1,057 words) - 19:33, 19 December 2012
• Ontology workflow
  ...ecause they facilitate consistent use of a term in annotation of disparate data types by different curators. Ontologies follow the convention that each te
  5 KB (862 words) - 19:20, 18 December 2012
• Adding Taxa to PaleoDB
  ...should have received training from the authorized person supervising your data entry. Note, as mentioned below, that names entered into the PaleDB do not ...dded since the last time the VTO was updated from the PaleoDB. In the ‘Data entry’ column under the heading ‘Basic steps’, click the ‘Add/edit
  6 KB (977 words) - 18:27, 16 July 2012
• API
  #REDIRECT [[Data Services]]
  27 bytes (3 words) - 01:05, 7 May 2012
• Knowledgebase tutorial
  ...ws, loaches, characins, and knifefishes), as well as developmental genetic data imported from [http://zfin.org/ ZFIN]. ...f interest, such as the “basihyal bone”. The KB consists of structured data in the form of related ontology terms. So the search field is used to find
  14 KB (2,237 words) - 19:06, 29 June 2016
• WG:Advisory Board Meeting 2012-12-04
• Issue trackers
  ==Provisional term (ORB) management web interface, data reports== https://github.com/phenoscape/phenoscape-data/issues
  655 bytes (95 words) - 21:37, 13 February 2013
• WG:PhenoScape monthly conference call/2012
• WG:PhenoScape monthly conference call/2011
• Bigdata
  ...ia the [[KB build process]] into a [[KB_build_process#RDF_data_model|graph data model]]. ...ass descriptions which share semantics to a greater degree than with other data items. For example, a gene may be associated with a set of phenotypic expre
  6 KB (898 words) - 18:17, 27 July 2015
• Data Availability
  #REDIRECT [[Phenoscape data policy]]
  36 bytes (4 words) - 23:10, 29 October 2014
• Postdoc2016
  ...sted in analyzing genomic and developmental data in relation to phenotypic data, with a focus on the vertebrate fin/limb. ...n). These data present a tremendous opportunity for integration with other data types to address questions about the evolution of phenotype.
  3 KB (444 words) - 18:13, 12 May 2016
• Resources for curators
  #REDIRECT [[Resources for Data Contributors]]
  45 bytes (5 words) - 21:18, 3 June 2016
• WG:PhenoScape monthly conference call/2014

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