pull changes made on master

LICENSE

@@ -0,0 +1,19 @@
+The MIT License 
+
+
+Copyright (c) 2010-2014, Hong Cui hongcui@email.arizona.edu 
+Copyright (c) 2010-2014, University of Arizona
+
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation 
+files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, 
+modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the 
+Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the 
+Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE 
+WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR 
+COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
+ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

README.md

@@ -1,28 +1,37 @@
 phenoscape-nlp
 ==============
 
-Source for EQ-Generating CharaParser application, which uses unsupervised lexicon learning and natural language processing to propose EQ-based phenotype annotations.
-It is useful for character descriptions written in the style similar to the example below:
+Source for [EQ]-Generating CharaParser application, which uses unsupervised lexicon learning and natural language processing to propose EQ-based phenotype annotations.
+The software is currently being developed as part of the Phenoscape project (http://phenoscape.org/). It is useful for character descriptions written in the style similar to the example below:
 
-Distal end of cleithrum
-
-1.is not bifurcate, bearing only an anterior process
-
-2.bifurcate
+> Distal end of cleithrum
+> 1. is not bifurcate, bearing only an anterior process
+> 2. bifurcate
 
 The input to EQ-Generating CharaParser is
 
 1. character descriptions in NeXML format
-
 2. a (may be empty) glossary of the related domain
-
 3. ontologies for EQs
 
-The software is currently being developed as part of the Phenoscape project (http://phenoscape.org/). 
-Source is provided with no warranty of any sort. 
-
 Some algorithms used in CharaParser are reported in:
 
-1. Cui, H., Boufford, D., & Selden, P. (2010). Semantic Annotation of Biosystematics Literature without Training Examples. Journal of American Society of Information Science and Technology. 61 (3): 522-542.http://onlinelibrary.wiley.com/doi/10.1002/asi.21246/full
+1. Cui, H., Boufford, D., & Selden, P. (2010). Semantic Annotation of Biosystematics Literature without Training Examples. Journal of American Society of Information Science and Technology. 61 (3): 522-542 [doi:10.1002/asi.21246]
+
+2. Cui, H. (2012). CharaParser for fine-grained semantic annotation of organism morphological descriptions. Journal of American Society of Information Science and Technology. 63(4) [doi:10.1002/asi.22618]
+
+License
+-------
+
+EQ-Generating CharaParser source code can be used, modified, and distributed under the terms of the MIT License. Please see the file LICENSE for details.
+
+How to cite
+-----------
+
+If you use EQ-Generating CharaParser in your research, please cite the following publications:
+
+•	Cui, H., Dahdul, W., Dececchi, A., Ibrahim, N., Mabee, P., Balhoff, J., Gopalakrishnan, H. (2015) CharaPaser+EQ: Performance Evaluation Without Gold Standard. Annual Meeting of the Association for Information Science and Technology, Nov 6-10, St Louis, Missouri, 2015. (Full paper, acceptance rate: 36.%) https://www.asist.org/files/meetings/am15/proceedings/openpage15.html
 
-2. Cui, H. (2012). CharaParser for fine-grained semantic annotation of organism morphological descriptions. Journal of American Society of Information Science and Technology. 63(4) DOI: 10.1002/asi.22618 http://onlinelibrary.wiley.com/doi/10.1002/asi.22618/pdf
+[EQ]: https://wiki.phenoscape.org/wiki/EQ_for_character_matrices
+[doi:10.1002/asi.21246]: http://doi.org/10.1002/asi.21246
+[doi:10.1002/asi.22618]: http://doi.org/10.1002/asi.22618

unsupervised/unsupervisedClauseMarkupBenchmarked.pl

@@ -175,9 +175,15 @@
 
 my $taglength = 150;
 
-my $host = "localhost";
-my $user = "biocreative";
-my $password = "biocreative";
+my $host = $ARGV[4];
+if(!$host){ $host = "localhost";}
+
+my $user = $ARGV[5];
+if(!$user){$user = "biocreative";}
+
+my $password = $ARGV[6];
+if(!$password){$password = "biocreative";}
+
 my $dbh = DBI->connect("DBI:mysql:host=$host", $user, $password)
 or die DBI->errstr."\n";