Create test_run_ami-search-cooccur20190120

test_run_ami-search-cooccur20190120

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+Documentation of test run of ami-search-cooccur over Ocimum sanctum test dataset.
+Introduction
+Contentmine is an open-source software suite for text data mining (content mining) especially of scientific journals. It is intended to benefit research based on literature survey in terms of high-throughput and accuracy.Here is documentation and tutorial related contentmine tools - Getpapers, norma and ami.
+Getpapers - It fatches scientific papers (full PDF or XML) along with metadata and supplementary informations. It performs first most step for content mining acquiring scientific papers for reading or bibliometrics.
+Norma - tool for processing the output of getpapers into normalized, tagged, XHTML or scholarly HTML which are further used as input for ami tools/plugins.
+AMI tools/plugins - Mining and analysis is performed by these tools or plugins. It searches and indexes structured documents on a high-throughput basis.
+
+Installation
+
+Tools are enabled for various computational platforms - Windows as well as Linux. Separate installation steps are discussed here.
+
+Getpapers installation over windows.
+step 1: Installing nvm-windows.
+Go to the downloads page - https://github.com/coreybutler/nvm-windows/releases  and download nvm-setup.zip for the latest version. Unzip the downloaded file and run the included installer.
+
+step 2: Run following commands over windows command-prompt.
+> nvm install 7
+> nvm use 7
+
+step 3: Installing a node tool - getpapers.
+> npm install --global getpapers
+
+step 4: Set environment variables to access installed getpapers tools.
+For example on my laptop it is installed into following directory.
+C:\Users\hadoop_pc\AppData\Roaming\npm
+
+Getpapapers installation over Linux.
+
+step 1: Installing nvm  
+> crl -o- https://raw.githubusercontent.com/creationix/nvm/v0.30.1/install.sh | bash
+Make sure of curl installation. (sudo apt-get install curl).
+or
+> wget -qO- https://raw.githubusercontent.com/creationix/nvm/v0.30.1/install.sh | bash
+
+step 2: Installing node
+Type following commands on to your terminal.
+>nvm install 7
+>nvm use 7
+>nvm alias default 7
+
+step 3: installing a node tool.
+
+>npm install --global getpapers
+
+AMI tool installation over windows.
+
+srep 1: Make your own installation area (directory containing the package).
+> mkdir AMI
+
+step 2: Get the ami software package into the directory.
+Download link - https://github.com/petermr/ami-jars
+
+step 3: Set environment variable to access the bin directory containing ami plugins/tools.
+To set environment variable in Windows - 08.
+               - From the desktop, right click the Computer icon.
+               - Choose System from the context menu.
+               - Click the Advanced system settings link.
+               - Click new option into user variables for desktop.
+               - Set variable name (environment variable name) and value (absolute path value).
+
+
+AMI tools installation over Linux.
+
+step 1: Make your own installation area (directory containing the package).
+> mkdir AMI
+
+step 2: Get the ami software package (clone ami repository into your area or directory).  
+> git clone https://github.com/petermr/ami-jars.git
+
+step 3: Set environmental variable to access the ami plugins (tools).
+Get into either of the directory ../ami-jar/ami20190115/bin/ or ../ami-jar/ami20190115/bin/ folder. All ami tools are contained into it. 
+Set the absolute path of the bin directory to environment variable.
+
+> export PATH=$PATH:/absolute path/ami-jar/ami20190115/bin/
+
+check for the set path to bin directory
+> echo $PATH
+
+5. Check for the installation.
+> ami-pdf
+If exported or installed correctly. It will list out all tool help information.
+
+Running steps for getpapers and ami plugins/tools.
+step 1: generate CProject.
+> getpapers -q <query_name> -o <project_folder>
+
+<query_name> - query name for the search (generally scientific names. These names are contained as dictionary into software suite.
+<project_folder> - name of the project folder (CProject). These contain the downloaded papers into PDF or XML format.
+
+step 2: Add scholarly.html file to CProject folders.
+> norma --project <project_folder> -i fulltext.xml -o scholarly.html --transform nlm2html
+
+step 3: Run ami plugins/tools.
+>ami-search-cooccur --project <project_folder>/ <plugin_options>
+<plugin_options> - space separated options for search e.g - country species gene plantparts drugs monoterpene.
+
+Test run over Ocimum Sanctum dataset.
+
+Here we run six getpapers queries for Ocimum sanctum dataset. It will form a subset of 100 papers. One may increase the number of count of downloaded papers just by changing the -k option of the command-line.
+
+> getpapers -q "Ocimum sanctum" -o osanctum20190121 -x -p -k 100
+> getpapers -q "ocimum" -o ocimum20190121 -x -p -k 100
+> getpapers -q "sanctum" -o sanctum20190121 -x -p -k 100
+> getpapers -q "ocimum AND sanctum" -o ocimumandsanctum20190121 -x -p -k 100
+> getpapers -q "ocimum sanctum" -o ocimum_sanctum20190121 -x -p -k 100
+> getpapers -q "((Ocimum sanctum) OR (Ocimum tenuiflorum) OR (thulasi) OR (tulasi) OR (tulsi) OR (holy basil))" -o ocimumsanctumadvancedsearch20190121 -x -p -k 100
+
+
+Perform normalization of downloaded papers and formation of scholarly HTML files.
+
+> norma --project osanctum20190121 -i fulltext.xml -o scholarly.html --transform nlm2html
+> norma --project ocimum20190121 -i fulltext.xml -o scholarly.html --transform nlm2html
+> norma --project sanctum20190121 -i fulltext.xml -o scholarly.html --transform nlm2html
+> norma --project ocimumandsanctum20190121 -i fulltext.xml -o scholarly.html --transform nlm2html
+> norma --project ocimum_sanctum20190121 -i fulltext.xml -o scholarly.html --transform nlm2html
+> norma --project ocimumsanctumadvancedsearch20190121 -i fulltext.xml -o scholarly.html --transform nlm2html
+
+Run ami plugin for search results.
+
+> ami-search-cooccur osanctum20190121/ country species drugs gene plantparts monoterpene
+> ami-search-cooccur ocimum20190121/ country species drugs gene plantparts monoterpene
+> ami-search-cooccur sanctum20190121/ country species drugs gene plantparts monoterpene
+> ami-search-cooccur ocimum_sanctum20190121/ country species drugs gene plantparts monoterpene 
+> ami-search-cooccur ocimumandsanctum20190121/ country species drugs gene plantparts monoterpene
+> ami-search-cooccur ocimumsanctumadvancedsearch20190121/ country species drugs gene plantparts monoterpene
+
+Results
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