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• Curation workflow
  ...he Phenoscape II Curation Log in Googledocs. Use the log to keep track of curation status for publications (what’s been done by who and when). # Upload PDF of paper to the Mendeley Vertebrate Curation Group
  6 KB (1,057 words) - 19:33, 19 December 2012

Page text matches

• Links
  ===Curation===
  4 KB (476 words) - 19:39, 24 May 2018
• Informatics
  ===Phenex curation tool=== ...d to load user-selected ontologies, and in this way can be adapted to data curation in different taxonomic groups.
  6 KB (808 words) - 22:14, 10 November 2012
• Ontologies
  ...o their pages). Taxonomic synonyms are particularly useful as aids to data curation, but common names can assist users in browsing the website. Taxonomic resou
  14 KB (2,022 words) - 17:42, 17 July 2018
• CharaParser
  [[Category:Curation]]
  1 KB (177 words) - 20:34, 26 March 2013
• Creating Taxon Lists
  # Update the curation log to indicate the work done on the taxon list. See below for example: [[I [[Category:Curation]]
  8 KB (1,303 words) - 20:56, 26 November 2012
• Fish Evolution Working Group
  ...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
• EQ for character matrices
  [[Category:Curation]]
  7 KB (1,089 words) - 23:42, 10 January 2009
• Phenote
  [[Category:Curation]]
  935 bytes (135 words) - 23:57, 10 January 2009
• Resources for Data Contributors
  ==3. Access PDFs for Curation == Phenoscape maintains a collection of PDFs for curation. Please ask project personnel (Wasila or Paula) for access to the collectio
  3 KB (364 words) - 01:17, 26 March 2019
• Phenote:Specimen List
  [[Category:Curation]]
  1 KB (178 words) - 23:58, 10 January 2009
• Phenote:Phylogeny Chooser
  [[Category:Curation]]
  2 KB (285 words) - 23:58, 10 January 2009
• Training and Workshops
  ...SICB09 Vision_sicb.pdf|Todd Vision]] - Software and database resources for curation and management of evolutionary phenotypes ...2009 are available to graduate students and postdocs for training in data curation and software development at NESCent and the University of South Dakota. [[
  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), Arighi et a ...Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex. Journal of Biomedical Semantics 5:45 [http://dx.doi.org/10.11
  52 KB (6,895 words) - 22:42, 17 November 2023
• EQ Editor requirements draft 1
  [[Category:Curation]]
  7 KB (1,124 words) - 23:41, 10 January 2009
• Documenting taxon concepts used in a publication
  [[Category:Curation]]
  1 KB (234 words) - 21:54, 22 November 2008
• Hypodigm
  [[Category:Curation]]
  2 KB (393 words) - 21:55, 22 November 2008
• Ontology Request Broker
  [[Category:Curation]]
  3 KB (457 words) - 18:07, 13 November 2015
• Needs Analysis Workshop/Summary
  ...ments for both our scientific framework/data model and our software tools (curation tools and web application). A good overview can also be found [[Needs Anal * Provide curation interface, storage, and analysis integration for private user data
  10 KB (1,445 words) - 05:23, 10 September 2008
• Data Jamboree 1
  ...project personnel focused on morphology, taxonomy, data curation, ontology curation, and informatics. The workshop will introduce ichthyologists to the approac The hands-on curation work at the jamboree will almost certainly reveal ontological issues, such
  9 KB (1,267 words) - 19:28, 11 January 2009
• Phenoscape data policy
  [[Category:Curation]]
  1 KB (174 words) - 13:39, 26 March 2019
• Guide to Character Annotation
  (Technical note: The use of ''present'' and ''absent'' in curation is a curatorial shortcut to the more logically sound syntax discussed on th '''**Note: Does not apply to current curation'''
  38 KB (5,768 words) - 05:13, 16 November 2016
• Data Jamboree 1/Annotation Experiment
  ...was conducted on day 2 of the April 2008 Data Jamboree in order to assess curation consistency among the four trained participants. Training consisted of a ha ...and inapplicable choices for terms and relations. Based on these results, curation standards and improvement to the Annotation Guide are in development, and i
  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 be quite cumbersome, particularly in [[Category: Curation]]
  13 KB (2,129 words) - 13:47, 9 September 2008
• Teleost Anatomy Ontology
  [[Category:Curation]]
  4 KB (661 words) - 01:37, 15 August 2012
• Creating and Editing Character Lists
  [[Category:Curation]]
  4 KB (615 words) - 20:04, 9 July 2008
• Term Requests
  [[Category:Curation]]
  7 KB (1,094 words) - 20:55, 30 September 2011
• Update Taxon Lists
  [[Category:Curation]]
  5 KB (759 words) - 21:14, 26 November 2012
• Data Jamboree 2
  ...Phenote and data entry; test/enhance curation consistency; further refine curation interface * Curation Exercise instructions (forthcoming)
  8 KB (1,022 words) - 20:08, 1 March 2011
• Data Jamboree 2/Agenda
  * 10:45 am: Curation Exercise (Wasila Dahdul) * 1:00 pm: Data curation: work on individual data
  3 KB (367 words) - 03:57, 7 October 2008
• Ontology-enabled reasoning across phenotypes from evolution and model organisms
  ...ments, by incorporating natural language processing tools and by improving curation software to allow for on-demand augmentation of community ontologies. [[Ima
  7 KB (945 words) - 20:11, 13 December 2019
• Data Jamboree 2/Preparation
  **Curation Exercise * Curation
  3 KB (392 words) - 17:43, 24 September 2008
• ZFIN anatomy annotation counts
  [[Category:Curation]]
  55 KB (8,568 words) - 00:02, 11 January 2009
• Data Jamboree 2/Notes
  ...curated, and importantly, versions of the ontologies that were used in the curation process (Mark Sabaj, Rick Mayden) == Notes from Data Curation Sessions ==
  19 KB (2,935 words) - 15:05, 14 October 2008
• Data Jamboree 2/Annotation Experiment
  ...genda | second data jamboree]]. The goals of the experiment were to assess curation consistency among a group of new curators, and to identify areas of improve * A hands-on, group curation exercise led and assisted by experienced curators given on the first day of
  7 KB (996 words) - 14:46, 8 October 2008
• Challenges in developing multi-species anatomy ontologies
  [[Category:Curation]]
  2 KB (274 words) - 23:44, 10 January 2009
• Front end user interface tools
  ===Phenex curation tool=== ...ll under development, Phenex is ready for use and enables our ongoing data curation activities.
  2 KB (256 words) - 23:48, 10 January 2009
• Problem Log Format
  ...eXML data, along with the ontological definitions of the terms used in the curation. Often, the curated files are in varying degrees of completeness comprising [[Category:Curation]]
  3 KB (365 words) - 23:59, 10 January 2009
• Annotation status
  [[Category:Curation]]
  6 KB (524 words) - 19:17, 3 May 2013
• Logic and Reasoning Challenges
  ...urrent definition of the ''PHENOSCAPE:exhibits'' relation is found. At the curation level, curators have to qualify their assertions as being either existentia [[Category:Curation]]
  18 KB (2,610 words) - 17:18, 22 February 2010
• Teleost Taxonomy Ontology
  ....org Fishbase]. Additional names and synonyms are added as a result of our curation activities.
  3 KB (401 words) - 19:25, 10 May 2017
• ORB term request prototype
  ...pplication that can launch new ontology term requests within existing data curation workflows, record term provenance and community discussion, enable temporar [[Category:Curation]]
  30 KB (4,747 words) - 13:13, 3 October 2010
• Synchronization Tool
  [[Category:Curation]]
  3 KB (526 words) - 22:05, 23 January 2009
• Novel reasoning strategies
  This strategy will require careful curation of the top level classes in the taxonomy. Definitions of higher level class
  8 KB (1,207 words) - 17:56, 29 June 2009
• Creating Tree Files
  [[Category:Curation]]
  2 KB (316 words) - 21:19, 26 November 2012
• SummerTraining2009
  ...Opportunities are available to work as part of the Phenoscape team on data curation or open source software/database development. Participants would be locate
  2 KB (323 words) - 02:51, 2 February 2009
• Student Instructions
  Phenex is used by Phenoscape for curation of evolutionary phenotypes. You can find instructions for downloading and * Phenoscape Curators mailing list (for discussion and communication of data curation issues, solutions, and progress): http://lists.sourceforge.net/lists/listi
  2 KB (253 words) - 20:06, 29 November 2012
• Entities with taxonomic context
  ==Impact on curation== [[Category:Curation]]
  4 KB (552 words) - 14:26, 30 March 2009
• ASIH09 workshop
  software for data curation (Phenex), and a knowledgebase that supports
  14 KB (1,979 words) - 14:02, 13 August 2009
• Phenotype Ontology Coordination Workshop
  *# Annotation group: What phenotype curation/annotation needs are there that are not adequately met? E.g. software, sta
  10 KB (1,285 words) - 02:21, 21 February 2011
• 2009 Grant Renewal Workshop
  #** Amphibanat: curation needs?
  7 KB (857 words) - 22:19, 10 February 2012
• Phenoscape Grant Renewal Workshop/Notes
  ** NLP-based text processing, Mass curation
  16 KB (2,313 words) - 17:34, 22 May 2009
• Acknowledgments
  ...and individuals have contributed to Phenoscape ontology development, data curation, workshops, and data entry: [[Category:Curation]]
  16 KB (2,112 words) - 23:44, 16 December 2019
• Author Guide
  [[Category:Curation]]
  4 KB (580 words) - 21:32, 15 June 2009
• Knowledgebase mockups (Nov 2009)
  ...designs are intended to support expansion of the list of qualities used in curation - as has already happened.
  7 KB (994 words) - 18:49, 21 January 2010
• Terminology
  ...cation (such as ''Danio'' sp. in Smith 1992). <font color=red>''- used in Curation paper''</font> [[Category:Curation]]
  4 KB (599 words) - 16:19, 4 June 2013
• SingleEntity TreeView
  ...designs are intended to support expansion of the list of qualities used in curation - as has already happened. ...designs are intended to support expansion of the list of qualities used in curation - as has already happened.
  2 KB (331 words) - 15:11, 28 January 2010
• Change And Correlation
  ...will need special treatment in any approach to incompatibility as current curation practice is to put them in comment strings.
  8 KB (1,097 words) - 20:55, 29 April 2010
• Knowledgebase Reports
  [[Category:Curation]]
  32 KB (4,884 words) - 15:32, 3 May 2012
• Reasoning over homology statements
  be used in phenoscape curation and reasoning. The core relation is the
  33 KB (5,448 words) - 22:33, 25 May 2018
• EQ shortcuts (temporary)
  Here are temporary curation shortcuts for creating particular kinds of phenotypes. These can be used un [[Category:Curation]]
  1 KB (163 words) - 02:07, 26 October 2010
• Matching Phenotypes
  ...t not have been captured, either in the original publication matrix or the curation process. For example, the absence of a Basihyal bone is observed in Siluri
  16 KB (2,382 words) - 17:40, 16 July 2012
• Anatomy Ontology Conf calls
  '''AMAO terms and curation''' * Paula: yes, and have terms done for curation of archosaur limb literature first
  31 KB (4,773 words) - 20:15, 13 March 2012
• Collaborative Phenotype Annotation
  ====Requirements from Phenoscape I curation workflow (that are expected to carry forward)==== ** real-time teaching of the curation tool, practices, and results to project curators
  12 KB (1,734 words) - 22:44, 18 September 2011
• Project Plan
  :; 1.1 NLP in aid of ontology building and EQ annotation : Curation of legacy phenotypes from the literature is a major bottleneck. The overall ...urces (PBDB, Paul's database, AmphibiaWeb). This ontology is required for curation of phenotypes and querying.
  9 KB (1,278 words) - 17:11, 28 August 2012
• Linking Evolution to Genomics Using Phenotype Ontologies
  ...ase with its web-interface, together with the extended ontologies and data curation tools, will allow researchers to ask novel questions about the genetic and ...lp of taxon experts for ostariophysan fishes, we prioritized 76 papers for curation; these can be viewed on our publicly available [http://spreadsheets.google.
  6 KB (922 words) - 18:05, 2 November 2011
• Software
  ==Data curation tools==
  9 KB (1,151 words) - 00:04, 10 December 2019
• KB data integrity checks
  [[Category:Curation]]
  862 bytes (119 words) - 21:41, 17 November 2011
• Phenoscape 1 Curated Publications
  [[Category:Curation]]
  11 KB (1,467 words) - 20:07, 11 November 2011
• To Edit is Divine
  * [[Curation]] page ** embed publicly accessible fin-limb phenotype curation log on [https://docs.google.com/spreadsheet/ccc?key=0Aj8NJdyb-leqdEhPRjgzak
  2 KB (317 words) - 20:44, 19 April 2012
• Curation workflow
  ...he Phenoscape II Curation Log in Googledocs. Use the log to keep track of curation status for publications (what’s been done by who and when). # Upload PDF of paper to the Mendeley Vertebrate Curation Group
  6 KB (1,057 words) - 19:33, 19 December 2012
• Annotator tutorial topics
  Overview of curation workflow and software involved ====Curation training====
  884 bytes (107 words) - 20:34, 29 November 2012
• Adding Taxa to PaleoDB
  [[Category:Curation]]
  6 KB (977 words) - 18:27, 16 July 2012