Difference between revisions of "BioPortal 2.1 (Core 1014; UI 1019) Release Notes"
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Benjamindai (talk | contribs) (Added bug fixes) |
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* Add syndication for a specific ontology | * Add syndication for a specific ontology | ||
* Filter out "[R].." relationships | * Filter out "[R].." relationships | ||
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=Resolved Bugs= | =Resolved Bugs= | ||
| − | 1157 Need to add "alpha" to "All Resources" tab | + | *1157 Need to add "alpha" to "All Resources" tab |
| − | 1159 Clicking on a Project in Projects tab results in an error | + | *1159 Clicking on a Project in Projects tab results in an error |
| − | 1194 Request to remove ontology - carol | + | *1194 Request to remove ontology - carol |
| − | 1188 Need isFoundry added to /ontologies response XML | + | *1188 Need isFoundry added to /ontologies response XML |
| − | 1153 Navigation Visualization doesn't scale correctly in IE | + | *1153 Navigation Visualization doesn't scale correctly in IE |
| − | 709 Additional inverse relationships gets introduced for OBO ontologies (has subclass and has part) | + | *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 | + | *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 | + | *1151 Full text name and/or description of resource |
| − | 1180 Wrong relations returned by a concept service in OBO ontologies | + | *1180 Wrong relations returned by a concept service in OBO ontologies |
| − | 1175 Category "Taxonomic Classification" has no instances | + | *1175 Category "Taxonomic Classification" has no instances |
| − | 1023 Ontology ID mismatch on metadata page and URL | + | *1023 Ontology ID mismatch on metadata page and URL |
| − | 1154 Wrong hierarchy when going directly to a concept in OWL ontologies | + | *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 | + | *1171 The children hierarchy service returns children only at the specified level, rather than *up to* specified level |
| − | 1148 Ontology selection - missing scroll bar | + | *1148 Ontology selection - missing scroll bar |
| − | 1150 Max Results slider | + | *1150 Max Results slider |
| − | 1163 Gene ontology not explorable on stage | + | *1163 Gene ontology not explorable on stage |
| − | 1161 Gene ontology not explorable | + | *1161 Gene ontology not explorable |
| − | 1132 Class details do not work in IE on Windows (hangs the browser) | + | *1132 Class details do not work in IE on Windows (hangs the browser) |
| − | 1145 OBO ontologies not explorable on the dev server | + | *1145 OBO ontologies not explorable on the dev server |
| − | 1108 [R]regulates link appear as "regulates" link in FlexViz | + | *1108 [R]regulates link appear as "regulates" link in FlexViz |
| − | 1097 Edit Metadata button - unable to add multiple categories | + | *1097 Edit Metadata button - unable to add multiple categories |
| − | 1127 NPO ontology is stuck in parsing | + | *1127 NPO ontology is stuck in parsing |
| − | 1118 Project page - updates needed for EFO project | + | *1118 Project page - updates needed for EFO project |
| − | 1109 Don't show "Thing" concept in Full FlexViz | + | *1109 Don't show "Thing" concept in Full FlexViz |
| − | 1110 Search of NCIT - not pointing to latest version | + | *1110 Search of NCIT - not pointing to latest version |
| − | 1117 EFO - stuck in Parsing | + | *1117 EFO - stuck in Parsing |
| − | 1098 Typo in message following ontology submission | + | *1098 Typo in message following ontology submission |
| − | 1121 Update the version number for NPO | + | *1121 Update the version number for NPO |
| − | 807 Ontology for disease genetic investigation Broken | + | *807 Ontology for disease genetic investigation Broken |
| − | 1092 Request to remove ontology - NIF Gross Anatomy | + | *1092 Request to remove ontology - NIF Gross Anatomy |
| − | 1084 STAGE - Error with term Clarke's nuclei in Jump to and Search | + | *1084 STAGE - Error with term Clarke's nuclei in Jump to and Search |
| − | 1095 Notes Column Overlap in IE and Safari | + | *1095 Notes Column Overlap in IE and Safari |
| − | 999 MySQL exceptions when requesting too many services | + | *999 MySQL exceptions when requesting too many services |
| − | 990 Update on ontologies with problem with the REST services | + | *990 Update on ontologies with problem with the REST services |
| − | 801 Ontology 38633 does not support UI | + | *801 Ontology 38633 does not support UI |
| − | 953 We should preserve namespaces with concepts in OWL ontologies, even when we use preferred names | + | *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 | + | *510 Adding ontologies to a project, maximize dialog doesn't use full screen |
| − | 1057 More concepts with problem (after processing of OBS DB) | + | *1057 More concepts with problem (after processing of OBS DB) |
| − | 835 Plus/Minus sign usage in Visualization full window is inconsistent | + | *835 Plus/Minus sign usage in Visualization full window is inconsistent |
| − | 486 A spurious phone number appears after user registration | + | *486 A spurious phone number appears after user registration |
| − | 991 Link to filter by group, should select menu highlight group filtered by? | + | *991 Link to filter by group, should select menu highlight group filtered by? |
| − | 800 Ontology 28837 does not support UI | + | *800 Ontology 28837 does not support UI |
| − | 961 Update on ontologies which has some conceptIDs as URL | + | *961 Update on ontologies which has some conceptIDs as URL |
| − | 1032 Duplication of ontology abbreviation on Home page for Gene Regulation ontology | + | *1032 Duplication of ontology abbreviation on Home page for Gene Regulation ontology |
| − | 984 Highly nested ontologies and tree-view | + | *984 Highly nested ontologies and tree-view |
| − | 1038 Notes expanded past note panel | + | *1038 Notes expanded past note panel |
| − | 1006 DermLex - issue with display of preferred name | + | *1006 DermLex - issue with display of preferred name |
| − | 974 Display of BioPortal metadata ontology? | + | *974 Display of BioPortal metadata ontology? |
| − | 596 In the Visualization tree: a click a node doesn't take move to that node | + | *596 In the Visualization tree: a click a node doesn't take move to that node |
| − | 1043 Repeated labels in OBI - {definition, definition} | + | *1043 Repeated labels in OBI - {definition, definition} |
| − | 511 Add Ontologies To Project dialog has too many scrollbars!! | + | *511 Add Ontologies To Project dialog has too many scrollbars!! |
| − | 551 Ontology review display and editing use ontology ID instead of ontology name | + | *551 Ontology review display and editing use ontology ID instead of ontology name |
| − | 925 Mapping not reciprocal - not shown for mapped to term | + | *925 Mapping not reciprocal - not shown for mapped to term |
| − | 554 When editing marginal notes the create link button doesn't work | + | *554 When editing marginal notes the create link button doesn't work |
| − | 613 Expanding tree view frame causing odd behaviour | + | *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 | + | *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. | + | *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 | + | *543 Need to stay on the same tab when exploring an ontology |
| − | 648 Concept tree navigation should be centered on the concept of focus | + | *648 Concept tree navigation should be centered on the concept of focus |
| − | 552 Ontology review feature is not working from the main ontology list | + | *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 | + | *587 When window width is reduced, columns jump to the bottom of it |
| − | 595 A clicked term has always the tab Details shown | + | *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 | + | *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? | + | *975 Are sessions used or automatic time-out? |
| − | 939 The note about the mappings should go on the mapping page | + | *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 | + | *1068 Request to remove versions of SO-PHARM that were not loaded correctly |
| − | + | *1079 MOD should be in the group PSI | |
| − | 1079 MOD should be in the group PSI | + | *1078 Ontology loading issues |
| − | 1078 Ontology loading issues | + | *808 Concept 4525/PathologicalPhenomenon makes BP REST services crashed |
| − | 808 Concept 4525/PathologicalPhenomenon makes BP REST services crashed | + | *563 Mappings download seems to not work all the time |
| − | 563 Mappings download seems to not work all the time | + | *1069 Unable to upload/submit new version of NCIT |
| − | 1069 Unable to upload/submit new version of NCIT | + | *816 Add link back to NCBO |
| − | 816 Add link back to NCBO | + | *605 OBO parse exception : LexBIG Ontology load failed |
| − | 605 OBO parse exception : LexBIG Ontology load failed | + | *851 Cannot specify Categories on the "Submit new ontology" page |
| − | 851 Cannot specify Categories on the "Submit new ontology" page | + | *1004 General Issue on 1/21/09 - local ontologies now remote |
| − | 1004 General Issue on 1/21/09 - local ontologies now remote | + | *1187 Separate multiple values by new line rather than comma |
| − | 1187 Separate multiple values by new line rather than comma | + | *1183 Do not show inverse relations on the Details page |
| − | 1183 Do not show inverse relations on the Details page | + | *1164 Resources - paging links to see list of resources from NextBio |
| − | 1164 Resources - paging links to see list of resources from NextBio | + | *1162 Alpha next to Resources not visible in tab name in IE |
| − | 1162 Alpha next to Resources not visible in tab name in IE | + | *1160 Add project button should be more prominent |
| − | 1160 Add project button should be more prominent | + | *1158 Help/about page doesn't have any margin |
| − | 1158 Help/about page doesn't have any margin | + | *1156 Virtual URLs for concepts don't work |
| − | 1156 Virtual URLs for concepts don't work | + | *1155 Change "MarginNote" to "Note" in the message after a note is created |
| − | 1155 Change "MarginNote" to "Note" in the message after a note is created | + | *1149 Semantic type - missing scroll bar |
| − | 1149 Semantic type - missing scroll bar | + | *1143 Projects and reviews not visible in Safari |
| − | 1143 Projects and reviews not visible in Safari | + | *1142 Length of Subject field for Notes |
| − | 1142 Length of Subject field for Notes | + | *1140 Wrong field for ontology upload on "Submit new version" |
| − | 1140 Wrong field for ontology upload on "Submit new version" | + | *1139 The "*fields are required" string is in the wrong place |
| − | 1139 The "*fields are required" string is in the wrong place | + | *1113 RSS feed for OBI has wrong id for URL |
| − | 1113 RSS feed for OBI has wrong id for URL | + | *1107 Send Feedback page |
| − | 1107 Send Feedback page | + | *1101 Email address usage for Support on BioPortal |
| − | 1101 Email address usage for Support on BioPortal | + | *1100 Request to remove Group MSI |
| − | 1100 Request to remove Group MSI | + | *1099 Explore button doesn't work on the new home page |
| − | 1099 Explore button doesn't work on the new home page | + | *1096 Filter mappings doesn't work on stage |
| − | 1096 Filter mappings doesn't work on stage | + | *1072 Need relationships on full path to root |
| − | 1072 Need relationships on full path to root | + | *1060 Unable to subscribe to overall BioPortal RSS feed |
| − | 1060 Unable to subscribe to overall BioPortal RSS feed | + | *1059 OBO ontologies parse errors causing wrong search results |
| − | 1059 OBO ontologies parse errors causing wrong search results | + | *1015 Need to add a note in order to see the past one |
| − | 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 |
| − | 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 |
| − | 957 Concepts with IDs starting with "@_" cannot be visualized in the UI | ||
Revision as of 10:59, 1 May 2009
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