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

• Annotator: a service that identifies mentions of biomedical ontology concepts in text that users submit. You can use the annotator service to tag automatically any item of interest with terms from UMLS and BioPortal ontologies. The Annotator is accessible via the BioPortal user interface and as a REST service

• Advanced ontology search user interface enables users to select which ontologies or categories of ontologies to search, specify search parameters, and filter and navigate easily through the search results

• Ontology-based projects: You can now describe your ontology-based projects, indicate which BioPortal ontologies you use, and provide reviews of those ontologies in the context of your project

• Version management for OWL ontologies: you can download a diff between successive versions of an OWL ontology in tab-delimited format or as a set of RDF instances of the Protégé Change and Annotations ontology. See, for example, the details for the Biomedical Resource Ontology, to see a listing of diffs for its versions.

• Within-ontology search: you can use the search box at the top of each ontology tree to type in preferred name or a synonym and jump directly to one of the concepts that matches your search term (look for the "Jump to" box when you are exploring an ontology)

• Support for different hierarchy relations in OBO format ontologies: just like in OBO-Edit, you will now see different icons when you browse the tree for an OBO ontologies, indicating the specific relationship between a child and a parent node (such as is-a or part-of)

• Numerous improvements in user interaction:
  • The new home page enables direct access to key BioPortal functionality, such as searching ontologies for terms, finding a specific ontology of interest, or searching the NCBO Resource index to find resources mentioning a particular concept of interest.
  • New look and feel for BioPortal user interface
  • Additional details on the ontology metadata page
  • It is now easier to add and view reviews for a particular ontology
  • Many other user interface improvements and fixes

• Prototypes of upcoming features for accessing the NCBO Resource index:
  • Access to biomedical resources annotated with a specific ontology term when you are viewing the term in BioPortal (in the "Resources" tab)
  • Search through all resource annotations available in the NCBO Resource index
  • The resources that NCBO currently indexes or provides access to include Conserved Domain Database, ArrayExpress, PharmGKB, UniProt KB, ARRS GoldMiner, Online Mendelian Inheritance in Man (OMIM), Reactome, Gene Expression Omnibus and NextBio (to check dynamically the list of resource that we currently have in the index, you can call the corresponding REST service).

• Links
  • Annotator http://bioportal.bioontology.org/annotate
  • Stand-alone Annotator REST web service http://bioontology.org/wiki/index.php/Annotator_Web_service
  • Advanced Ontology Search http://bioportal.bioontology.org/search
  • Ontology-based Projects http://bioportal.bioontology.org/projects
  • Biomedical Resource Ontology http://bioportal.bioontology.org/ontologies/39521
  • NCBO Resource Index http://ncbolabs-dev2.stanford.edu:8080/OBS_v1/obr/resources

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