BioPortal 2.1 (Core 1014; UI 1019) Release Notes

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

• 1153 Navigation Visualization doesn't scale correctly in IE
• 1157 Need to add "alpha" to "All Resources" tab
• 1159 Clicking on a Project in Projects tab results in an error
• 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
• 1194 Request to remove ontology
• 1188 Need isFoundry added to /ontologies response XML
• 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