BioPortal 2.1 (Core 1014; UI 1019) Release Notes

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Revision as of 09:59, 1 May 2009 by Benjamindai (talk | contribs) (Added bug fixes)
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BioPortal 2.1 consists of two NCBO software packages: BioPortal Core (Label 1014) and BioPortal UI (Label 1019).

New Features

  • New Annotator service
  • New All Resources UI
  • New Search UI
  • New BioPortal Look and Feel
  • New labels on relations in the tree
  • Adding reviews and projects
  • Ontology list on the Browse page
  • Add column on main page for group
  • Add syndication for a specific ontology
  • Filter out "[R].." relationships

Resolved Bugs

  • 1157 Need to add "alpha" to "All Resources" tab
  • 1159 Clicking on a Project in Projects tab results in an error
  • 1194 Request to remove ontology - carol
  • 1188 Need isFoundry added to /ontologies response XML
  • 1153 Navigation Visualization doesn't scale correctly in IE
  • 709 Additional inverse relationships gets introduced for OBO ontologies (has subclass and has part)
  • 1131 Explore button on home page should take you to the metadata page for ontologies that are not explorable
  • 1151 Full text name and/or description of resource
  • 1180 Wrong relations returned by a concept service in OBO ontologies
  • 1175 Category "Taxonomic Classification" has no instances
  • 1023 Ontology ID mismatch on metadata page and URL
  • 1154 Wrong hierarchy when going directly to a concept in OWL ontologies
  • 1171 The children hierarchy service returns children only at the specified level, rather than *up to* specified level
  • 1148 Ontology selection - missing scroll bar
  • 1150 Max Results slider
  • 1163 Gene ontology not explorable on stage
  • 1161 Gene ontology not explorable
  • 1132 Class details do not work in IE on Windows (hangs the browser)
  • 1145 OBO ontologies not explorable on the dev server
  • 1108 [R]regulates link appear as "regulates" link in FlexViz
  • 1097 Edit Metadata button - unable to add multiple categories
  • 1127 NPO ontology is stuck in parsing
  • 1118 Project page - updates needed for EFO project
  • 1109 Don't show "Thing" concept in Full FlexViz
  • 1110 Search of NCIT - not pointing to latest version
  • 1117 EFO - stuck in Parsing
  • 1098 Typo in message following ontology submission
  • 1121 Update the version number for NPO
  • 807 Ontology for disease genetic investigation Broken
  • 1092 Request to remove ontology - NIF Gross Anatomy
  • 1084 STAGE - Error with term Clarke's nuclei in Jump to and Search
  • 1095 Notes Column Overlap in IE and Safari
  • 999 MySQL exceptions when requesting too many services
  • 990 Update on ontologies with problem with the REST services
  • 801 Ontology 38633 does not support UI
  • 953 We should preserve namespaces with concepts in OWL ontologies, even when we use preferred names
  • 510 Adding ontologies to a project, maximize dialog doesn't use full screen
  • 1057 More concepts with problem (after processing of OBS DB)
  • 835 Plus/Minus sign usage in Visualization full window is inconsistent
  • 486 A spurious phone number appears after user registration
  • 991 Link to filter by group, should select menu highlight group filtered by?
  • 800 Ontology 28837 does not support UI
  • 961 Update on ontologies which has some conceptIDs as URL
  • 1032 Duplication of ontology abbreviation on Home page for Gene Regulation ontology
  • 984 Highly nested ontologies and tree-view
  • 1038 Notes expanded past note panel
  • 1006 DermLex - issue with display of preferred name
  • 974 Display of BioPortal metadata ontology?
  • 596 In the Visualization tree: a click a node doesn't take move to that node
  • 1043 Repeated labels in OBI - {definition, definition}
  • 511 Add Ontologies To Project dialog has too many scrollbars!!
  • 551 Ontology review display and editing use ontology ID instead of ontology name
  • 925 Mapping not reciprocal - not shown for mapped to term
  • 554 When editing marginal notes the create link button doesn't work
  • 613 Expanding tree view frame causing odd behaviour
  • 497 If I select a particular tab (e.g., Details), then this tab should open when I click on a different class
  • 547 Clicking on a node on the graph view should open the corresponding concept.
  • 543 Need to stay on the same tab when exploring an ontology
  • 648 Concept tree navigation should be centered on the concept of focus
  • 552 Ontology review feature is not working from the main ontology list
  • 587 When window width is reduced, columns jump to the bottom of it
  • 595 A clicked term has always the tab Details shown
  • 628 Marginal Note - Title Field in Comment Display is too short (i.e., Comment Editor is significantly longer than display) and Missing Comments
  • 975 Are sessions used or automatic time-out?
  • 939 The note about the mappings should go on the mapping page
  • 1068 Request to remove versions of SO-PHARM that were not loaded correctly
  • 1079 MOD should be in the group PSI
  • 1078 Ontology loading issues
  • 808 Concept 4525/PathologicalPhenomenon makes BP REST services crashed
  • 563 Mappings download seems to not work all the time
  • 1069 Unable to upload/submit new version of NCIT
  • 816 Add link back to NCBO
  • 605 OBO parse exception : LexBIG Ontology load failed
  • 851 Cannot specify Categories on the "Submit new ontology" page
  • 1004 General Issue on 1/21/09 - local ontologies now remote
  • 1187 Separate multiple values by new line rather than comma
  • 1183 Do not show inverse relations on the Details page
  • 1164 Resources - paging links to see list of resources from NextBio
  • 1162 Alpha next to Resources not visible in tab name in IE
  • 1160 Add project button should be more prominent
  • 1158 Help/about page doesn't have any margin
  • 1156 Virtual URLs for concepts don't work
  • 1155 Change "MarginNote" to "Note" in the message after a note is created
  • 1149 Semantic type - missing scroll bar
  • 1143 Projects and reviews not visible in Safari
  • 1142 Length of Subject field for Notes
  • 1140 Wrong field for ontology upload on "Submit new version"
  • 1139 The "*fields are required" string is in the wrong place
  • 1113 RSS feed for OBI has wrong id for URL
  • 1107 Send Feedback page
  • 1101 Email address usage for Support on BioPortal
  • 1100 Request to remove Group MSI
  • 1099 Explore button doesn't work on the new home page
  • 1096 Filter mappings doesn't work on stage
  • 1072 Need relationships on full path to root
  • 1060 Unable to subscribe to overall BioPortal RSS feed
  • 1059 OBO ontologies parse errors causing wrong search results
  • 1015 Need to add a note in order to see the past one
  • 971 When a user creates a note, it does not show up right away
  • 957 Concepts with IDs starting with "@_" cannot be visualized in the UI