[jira] Updated: (UIMA-1639) Fixed bugs which disabled compiled dicts, static dict attributes
[ https://issues.apache.org/jira/browse/UIMA-1639?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Michael Tanenblatt updated UIMA-1639: - Attachment: EntryPropertiesRoot.java org/apache/uima/conceptMapper/support/dictionaryResource/EntryPropertiesRoot.java for repository > Fixed bugs which disabled compiled dicts, static dict attributes > > > Key: UIMA-1639 > URL: https://issues.apache.org/jira/browse/UIMA-1639 > Project: UIMA > Issue Type: Bug > Components: Sandbox-ConceptMapper >Reporter: Michael Tanenblatt > Attachments: CM-patch-20091027.txt, EntryPropertiesRoot.java > > -- This message is automatically generated by JIRA. - You can reply to this email to add a comment to the issue online.
[jira] Updated: (UIMA-1639) Fixed bugs which disabled compiled dicts, static dict attributes
[ https://issues.apache.org/jira/browse/UIMA-1639?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Michael Tanenblatt updated UIMA-1639: - Attachment: CM-patch-20091027.txt > Fixed bugs which disabled compiled dicts, static dict attributes > > > Key: UIMA-1639 > URL: https://issues.apache.org/jira/browse/UIMA-1639 > Project: UIMA > Issue Type: Bug > Components: Sandbox-ConceptMapper >Reporter: Michael Tanenblatt > Attachments: CM-patch-20091027.txt > > -- This message is automatically generated by JIRA. - You can reply to this email to add a comment to the issue online.
[jira] Created: (UIMA-1639) Fixed bugs which disabled compiled dicts, static dict attributes
Fixed bugs which disabled compiled dicts, static dict attributes Key: UIMA-1639 URL: https://issues.apache.org/jira/browse/UIMA-1639 Project: UIMA Issue Type: Bug Components: Sandbox-ConceptMapper Reporter: Michael Tanenblatt -- This message is automatically generated by JIRA. - You can reply to this email to add a comment to the issue online.
[jira] Updated: (UIMA-1605) Fixed Findbugs issues
[ https://issues.apache.org/jira/browse/UIMA-1605?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Michael Tanenblatt updated UIMA-1605: - Attachment: patch20091009-corrected.txt Corrected patch file (?) > Fixed Findbugs issues > - > > Key: UIMA-1605 > URL: https://issues.apache.org/jira/browse/UIMA-1605 > Project: UIMA > Issue Type: Bug > Components: Sandbox-ConceptMapper >Reporter: Michael Tanenblatt >Assignee: Marshall Schor >Priority: Minor > Attachments: patch20091009-corrected.txt, patch20091009.txt > > > Corrected a few issues discovered by Findbugs. -- This message is automatically generated by JIRA. - You can reply to this email to add a comment to the issue online.
[jira] Updated: (UIMA-1605) Fixed Findbugs issues
[ https://issues.apache.org/jira/browse/UIMA-1605?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Michael Tanenblatt updated UIMA-1605: - Attachment: patch20091009.txt > Fixed Findbugs issues > - > > Key: UIMA-1605 > URL: https://issues.apache.org/jira/browse/UIMA-1605 > Project: UIMA > Issue Type: Bug > Components: Sandbox-ConceptMapper >Reporter: Michael Tanenblatt >Priority: Minor > Attachments: patch20091009.txt > > > Corrected a few issues discovered by Findbugs. -- This message is automatically generated by JIRA. - You can reply to this email to add a comment to the issue online.
[jira] Created: (UIMA-1605) Fixed Findbugs issues
Fixed Findbugs issues - Key: UIMA-1605 URL: https://issues.apache.org/jira/browse/UIMA-1605 Project: UIMA Issue Type: Bug Components: Sandbox-ConceptMapper Reporter: Michael Tanenblatt Priority: Minor Attachments: patch20091009.txt Corrected a few issues discovered by Findbugs. -- This message is automatically generated by JIRA. - You can reply to this email to add a comment to the issue online.
[jira] Updated: (UIMA-1498) if an exception is rethrown, the original exception is not currently passed through
[ https://issues.apache.org/jira/browse/UIMA-1498?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Michael Tanenblatt updated UIMA-1498: - Attachment: patch.txt This patch resolves the issue > if an exception is rethrown, the original exception is not currently passed > through > --- > > Key: UIMA-1498 > URL: https://issues.apache.org/jira/browse/UIMA-1498 > Project: UIMA > Issue Type: Improvement > Components: Sandbox-ConceptMapper >Reporter: Michael Tanenblatt >Priority: Minor > Attachments: patch.txt > > > if an exception is rethrown, the original exception is not currently passed > through -- This message is automatically generated by JIRA. - You can reply to this email to add a comment to the issue online.
[jira] Created: (UIMA-1498) if an exception is rethrown, the original exception is not currently passed through
if an exception is rethrown, the original exception is not currently passed through --- Key: UIMA-1498 URL: https://issues.apache.org/jira/browse/UIMA-1498 Project: UIMA Issue Type: Improvement Components: Sandbox-ConceptMapper Reporter: Michael Tanenblatt Priority: Minor if an exception is rethrown, the original exception is not currently passed through -- This message is automatically generated by JIRA. - You can reply to this email to add a comment to the issue online.
[jira] Closed: (UIMA-1371) Performance improvement: remove reliance on Property class and excess String building to reduce in-memory dictionary size.
[ https://issues.apache.org/jira/browse/UIMA-1371?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Michael Tanenblatt closed UIMA-1371. > Performance improvement: remove reliance on Property class and excess String > building to reduce in-memory dictionary size. > -- > > Key: UIMA-1371 > URL: https://issues.apache.org/jira/browse/UIMA-1371 > Project: UIMA > Issue Type: New Feature > Components: Sandbox-ConceptMapper > Environment: All >Reporter: Michael Tanenblatt >Assignee: Michael Tanenblatt > Attachments: cm-patch20090605.txt > > > Performance improvement: remove reliance on Property class and excess String > building to reduce in-memory dictionary size. -- This message is automatically generated by JIRA. - You can reply to this email to add a comment to the issue online.
[jira] Created: (UIMA-1372) Improve description of ConceptMapper on UIMA sandbox components web page
Improve description of ConceptMapper on UIMA sandbox components web page Key: UIMA-1372 URL: https://issues.apache.org/jira/browse/UIMA-1372 Project: UIMA Issue Type: Improvement Environment: all Reporter: Michael Tanenblatt Here is the proposed new wording: ConceptMapper is a powerful, highly configurable dictionary UIMA-based annotator. Numerous parameters can be used to specify various aspects of the lookup algorithm, input processing and output options. The dictionary structure is flexible, allowing any number synonyms to be associated with an entry, and any number of attributes to be associated with entries or synonyms. Lookup and matching against dictionary entries can be performed against contiguous or non-contiguous blocks of text, and token order independant lookup is also allowed (for example, the tokens "A" "B" would be considered a match against dictionary entry "B" "A"). Additionally, ConceptMapper can be configured to use any tokenizer annotator, enabling tokenization of its dictionaries identically with the input text. -- This message is automatically generated by JIRA. - You can reply to this email to add a comment to the issue online.
[jira] Updated: (UIMA-1371) Performance improvement: remove reliance on Property class and excess String building to reduce in-memory dictionary size.
[ https://issues.apache.org/jira/browse/UIMA-1371?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Michael Tanenblatt updated UIMA-1371: - Attachment: cm-patch20090605.txt addresses issues in UIMA-1371 > Performance improvement: remove reliance on Property class and excess String > building to reduce in-memory dictionary size. > -- > > Key: UIMA-1371 > URL: https://issues.apache.org/jira/browse/UIMA-1371 > Project: UIMA > Issue Type: New Feature > Components: Sandbox-ConceptMapper > Environment: All >Reporter: Michael Tanenblatt > Attachments: cm-patch20090605.txt > > > Performance improvement: remove reliance on Property class and excess String > building to reduce in-memory dictionary size. -- This message is automatically generated by JIRA. - You can reply to this email to add a comment to the issue online.
[jira] Created: (UIMA-1371) Performance improvement: remove reliance on Property class and excess String building to reduce in-memory dictionary size.
Performance improvement: remove reliance on Property class and excess String building to reduce in-memory dictionary size. -- Key: UIMA-1371 URL: https://issues.apache.org/jira/browse/UIMA-1371 Project: UIMA Issue Type: New Feature Components: Sandbox-ConceptMapper Environment: All Reporter: Michael Tanenblatt Performance improvement: remove reliance on Property class and excess String building to reduce in-memory dictionary size. -- This message is automatically generated by JIRA. - You can reply to this email to add a comment to the issue online.
[jira] Updated: (UIMA-1336) allow multiple dictionary entries to match against a single string
[ https://issues.apache.org/jira/browse/UIMA-1336?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Michael Tanenblatt updated UIMA-1336: - Attachment: CM-multireturn-patch.txt This patch fixes the issue > allow multiple dictionary entries to match against a single string > -- > > Key: UIMA-1336 > URL: https://issues.apache.org/jira/browse/UIMA-1336 > Project: UIMA > Issue Type: Improvement > Components: Sandbox-ConceptMapper >Reporter: Michael Tanenblatt > Attachments: CM-multireturn-patch.txt > > > If multiple dictionary entries contain the same text, only one will be > selected to match against the input text, even if the parameter > "FindAllMatches" is set to true -- This message is automatically generated by JIRA. - You can reply to this email to add a comment to the issue online.
[jira] Created: (UIMA-1336) allow multiple dictionary entries to match against a single string
allow multiple dictionary entries to match against a single string -- Key: UIMA-1336 URL: https://issues.apache.org/jira/browse/UIMA-1336 Project: UIMA Issue Type: Improvement Components: Sandbox-ConceptMapper Reporter: Michael Tanenblatt If multiple dictionary entries contain the same text, only one will be selected to match against the input text, even if the parameter "FindAllMatches" is set to true -- This message is automatically generated by JIRA. - You can reply to this email to add a comment to the issue online.
[jira] Updated: (UIMA-1301) Update documentation, log problems when dictionary entries don't load, remove diagnostic message during dictionary loading
[ https://issues.apache.org/jira/browse/UIMA-1301?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Michael Tanenblatt updated UIMA-1301: - Attachment: ConceptMapper20090311Patch.txt > Update documentation, log problems when dictionary entries don't load, remove > diagnostic message during dictionary loading > -- > > Key: UIMA-1301 > URL: https://issues.apache.org/jira/browse/UIMA-1301 > Project: UIMA > Issue Type: Improvement > Components: Sandbox-ConceptMapper >Reporter: Michael Tanenblatt > Attachments: ConceptMapper20090311Patch.txt > > -- This message is automatically generated by JIRA. - You can reply to this email to add a comment to the issue online.
[jira] Created: (UIMA-1301) Update documentation, log problems when dictionary entries don't load, remove diagnostic message during dictionary loading
Update documentation, log problems when dictionary entries don't load, remove diagnostic message during dictionary loading -- Key: UIMA-1301 URL: https://issues.apache.org/jira/browse/UIMA-1301 Project: UIMA Issue Type: Improvement Components: Sandbox-ConceptMapper Reporter: Michael Tanenblatt -- This message is automatically generated by JIRA. - You can reply to this email to add a comment to the issue online.
[jira] Commented: (UIMA-1033) ConceptMapper--a highly configurable, token-based dictionary lookup UIMA component
[ https://issues.apache.org/jira/browse/UIMA-1033?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=12597986#action_12597986 ] Michael Tanenblatt commented on UIMA-1033: -- Sorry about that missing uima.tt.TokenAnnotation--I must have done that in an overexuberant fit of cleaning! As to future plans: we use ConceptMapper extensively in our projects, and am certainly interested in helping maintain and enhance it as needed, time permitting. > ConceptMapper--a highly configurable, token-based dictionary lookup UIMA > component > -- > > Key: UIMA-1033 > URL: https://issues.apache.org/jira/browse/UIMA-1033 > Project: UIMA > Issue Type: New Feature > Components: Sandbox > Environment: Java 5 >Reporter: Michael Tanenblatt >Priority: Minor > Attachments: conceptMapper.zip, conceptMapper.zip.md5 > > Original Estimate: 24h > Remaining Estimate: 24h > > ConceptMapper is a token-based dictionary lookup UIMA component. It was > designed specifically to allow any external tokenizer that is a UIMA > component to be used to tokenize its dictionary. Using the same tokenizer > on both the dictionary and for subsequent text processing prevents > situations where a particular dictionary entry is not found, though it > exists, because it was tokenized differently than the text being processed. > ConceptMapper is highly configurable, in terms of: > * the way dictionary entries are mapped to resultant annotations > * the way input documents are processed > * the availability of multiple lookup strategies > * its various output options. > Additionally, a set of post-processing filters are supplied, as well as an > interface to easily create new filters. This allows for overgenerating > results during the lookup phase, if so desired, then reducing the result > set according to particular rules. > More details: > The structure of the dictionary itself is quite flexible. Entries can have > any number of variants (synonyms), and arbitrary features can be associated > with dictionary entries. Individual variants inherit features from parent > token (i.e., the canonical from), but can override them or add additional > features. In the following sample dictionary entry, there are 5 variants of > the canonical form, and as described earlier, each inherits the SemClass > and POS attributes from the canonical form, with the exception of the > variant "mesenteric fibromatosis (c48.1)", which overrides the value of the > SemClass attribute (this is somewhat of a contrived example, just to make > that point): > > > > SemClass="Diagnosis-Site" /> > > > > Input tokens are processed one span at a time, where both the token and > span (usually a sentence) annotation type are configurable. Additionally, > the particular feature of the token annotation to use for lookups can be > specified, otherwise its covered text is used. Other input configuration > settings are whether to use case sensitive matching, an optional class name > of a stemmer to apply to the tokens, and a list of stop words to to ignore > during lookup. One additional input control mechanism is the ability to > skip tokens during lookups based on particular feature values. In this way, > it is easy to skip, for example, all tokens with particular part of speech > tags, or with some previously computed semantic class. > Output is in the form of new annotations, and the type of resulting > annotations can be specified in a descriptor file. The mapping from > dictionary entry attributes to the result annotation features can also be > specified. Additionally, a string containing the matched text, a list of > matched tokens, and the span enclosing the match can be specified to be set > in the result annotations. It is also possible to indicate dictionary > attributes to write back into each of the matched tokens. > Dictionary lookup is controlled by three parameters in the descriptor, one > of which allows for order-independent lookup (i.e., A B == B A), another > togles between finding only the longest match vs. finding all possible > matches. The final parameter specifies the search strategy, of which there > are three. The default search strategy only considers contiguous tokens > (not including tokens frm the stop word list or otherwise skipped tokens), > and then begins the subsequent search after the longest match. The second > strategy allows for ignoring non-matching tokens, allowing for disjoint > matches, so that a dictionary entry of > A C > would match against the text > A B C > As with the default search strategy, the subsequent search begins after the > longest match. The final search strategy is identical to the previous, > except that subsequent searches begin one
[jira] Updated: (UIMA-1033) ConceptMapper--a highly configurable, token-based dictionary lookup UIMA component
[ https://issues.apache.org/jira/browse/UIMA-1033?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Michael Tanenblatt updated UIMA-1033: - Attachment: conceptMapper.zip.md5 conceptMapper.zip Source and md5 signature of ConceptMapper > ConceptMapper--a highly configurable, token-based dictionary lookup UIMA > component > -- > > Key: UIMA-1033 > URL: https://issues.apache.org/jira/browse/UIMA-1033 > Project: UIMA > Issue Type: New Feature > Components: Sandbox > Environment: Java 5 >Reporter: Michael Tanenblatt >Priority: Minor > Attachments: conceptMapper.zip, conceptMapper.zip.md5 > > Original Estimate: 24h > Remaining Estimate: 24h > > ConceptMapper is a token-based dictionary lookup UIMA component. It was > designed specifically to allow any external tokenizer that is a UIMA > component to be used to tokenize its dictionary. Using the same tokenizer > on both the dictionary and for subsequent text processing prevents > situations where a particular dictionary entry is not found, though it > exists, because it was tokenized differently than the text being processed. > ConceptMapper is highly configurable, in terms of: > * the way dictionary entries are mapped to resultant annotations > * the way input documents are processed > * the availability of multiple lookup strategies > * its various output options. > Additionally, a set of post-processing filters are supplied, as well as an > interface to easily create new filters. This allows for overgenerating > results during the lookup phase, if so desired, then reducing the result > set according to particular rules. > More details: > The structure of the dictionary itself is quite flexible. Entries can have > any number of variants (synonyms), and arbitrary features can be associated > with dictionary entries. Individual variants inherit features from parent > token (i.e., the canonical from), but can override them or add additional > features. In the following sample dictionary entry, there are 5 variants of > the canonical form, and as described earlier, each inherits the SemClass > and POS attributes from the canonical form, with the exception of the > variant "mesenteric fibromatosis (c48.1)", which overrides the value of the > SemClass attribute (this is somewhat of a contrived example, just to make > that point): > > > > SemClass="Diagnosis-Site" /> > > > > Input tokens are processed one span at a time, where both the token and > span (usually a sentence) annotation type are configurable. Additionally, > the particular feature of the token annotation to use for lookups can be > specified, otherwise its covered text is used. Other input configuration > settings are whether to use case sensitive matching, an optional class name > of a stemmer to apply to the tokens, and a list of stop words to to ignore > during lookup. One additional input control mechanism is the ability to > skip tokens during lookups based on particular feature values. In this way, > it is easy to skip, for example, all tokens with particular part of speech > tags, or with some previously computed semantic class. > Output is in the form of new annotations, and the type of resulting > annotations can be specified in a descriptor file. The mapping from > dictionary entry attributes to the result annotation features can also be > specified. Additionally, a string containing the matched text, a list of > matched tokens, and the span enclosing the match can be specified to be set > in the result annotations. It is also possible to indicate dictionary > attributes to write back into each of the matched tokens. > Dictionary lookup is controlled by three parameters in the descriptor, one > of which allows for order-independent lookup (i.e., A B == B A), another > togles between finding only the longest match vs. finding all possible > matches. The final parameter specifies the search strategy, of which there > are three. The default search strategy only considers contiguous tokens > (not including tokens frm the stop word list or otherwise skipped tokens), > and then begins the subsequent search after the longest match. The second > strategy allows for ignoring non-matching tokens, allowing for disjoint > matches, so that a dictionary entry of > A C > would match against the text > A B C > As with the default search strategy, the subsequent search begins after the > longest match. The final search strategy is identical to the previous, > except that subsequent searches begin one token ahead, instead of after the > previous match. This enables overlapped matching. -- This message is automatically generated by JIRA. - You can reply to this email to add a comment to the issue online.
[jira] Created: (UIMA-1033) ConceptMapper--a highly configurable, token-based dictionary lookup UIMA component
ConceptMapper--a highly configurable, token-based dictionary lookup UIMA component -- Key: UIMA-1033 URL: https://issues.apache.org/jira/browse/UIMA-1033 Project: UIMA Issue Type: New Feature Components: Sandbox Environment: Java 5 Reporter: Michael Tanenblatt Priority: Minor ConceptMapper is a token-based dictionary lookup UIMA component. It was designed specifically to allow any external tokenizer that is a UIMA component to be used to tokenize its dictionary. Using the same tokenizer on both the dictionary and for subsequent text processing prevents situations where a particular dictionary entry is not found, though it exists, because it was tokenized differently than the text being processed. ConceptMapper is highly configurable, in terms of: * the way dictionary entries are mapped to resultant annotations * the way input documents are processed * the availability of multiple lookup strategies * its various output options. Additionally, a set of post-processing filters are supplied, as well as an interface to easily create new filters. This allows for overgenerating results during the lookup phase, if so desired, then reducing the result set according to particular rules. More details: The structure of the dictionary itself is quite flexible. Entries can have any number of variants (synonyms), and arbitrary features can be associated with dictionary entries. Individual variants inherit features from parent token (i.e., the canonical from), but can override them or add additional features. In the following sample dictionary entry, there are 5 variants of the canonical form, and as described earlier, each inherits the SemClass and POS attributes from the canonical form, with the exception of the variant "mesenteric fibromatosis (c48.1)", which overrides the value of the SemClass attribute (this is somewhat of a contrived example, just to make that point): Input tokens are processed one span at a time, where both the token and span (usually a sentence) annotation type are configurable. Additionally, the particular feature of the token annotation to use for lookups can be specified, otherwise its covered text is used. Other input configuration settings are whether to use case sensitive matching, an optional class name of a stemmer to apply to the tokens, and a list of stop words to to ignore during lookup. One additional input control mechanism is the ability to skip tokens during lookups based on particular feature values. In this way, it is easy to skip, for example, all tokens with particular part of speech tags, or with some previously computed semantic class. Output is in the form of new annotations, and the type of resulting annotations can be specified in a descriptor file. The mapping from dictionary entry attributes to the result annotation features can also be specified. Additionally, a string containing the matched text, a list of matched tokens, and the span enclosing the match can be specified to be set in the result annotations. It is also possible to indicate dictionary attributes to write back into each of the matched tokens. Dictionary lookup is controlled by three parameters in the descriptor, one of which allows for order-independent lookup (i.e., A B == B A), another togles between finding only the longest match vs. finding all possible matches. The final parameter specifies the search strategy, of which there are three. The default search strategy only considers contiguous tokens (not including tokens frm the stop word list or otherwise skipped tokens), and then begins the subsequent search after the longest match. The second strategy allows for ignoring non-matching tokens, allowing for disjoint matches, so that a dictionary entry of A C would match against the text A B C As with the default search strategy, the subsequent search begins after the longest match. The final search strategy is identical to the previous, except that subsequent searches begin one token ahead, instead of after the previous match. This enables overlapped matching. -- This message is automatically generated by JIRA. - You can reply to this email to add a comment to the issue online.
