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        "author": "Chris Churas",
        "author_email": "contact@ndexbio.org",
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        "classifiers": [
            "Development Status :: 2 - Pre-Alpha",
            "Intended Audience :: Developers",
            "License :: OSI Approved :: BSD License",
            "Natural Language :: English",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: 3.5",
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        "description": "===========================\nNDEx NCI-PID content loader\n===========================\n\n\n.. image:: https://img.shields.io/pypi/v/ndexncipidloader.svg\n        :target: https://pypi.python.org/pypi/ndexncipidloader\n\n.. image:: https://img.shields.io/travis/ndexcontent/ndexncipidloader.svg\n        :target: https://travis-ci.org/ndexcontent/ndexncipidloader\n\n.. image:: https://coveralls.io/repos/github/ndexcontent/ndexncipidloader/badge.svg?branch=master\n        :target: https://coveralls.io/github/ndexcontent/ndexncipidloader?branch=master\n\n.. image:: https://readthedocs.org/projects/ndexncipidloader/badge/?version=latest\n        :target: https://ndexncipidloader.readthedocs.io/en/latest/?badge=latest\n        :alt: Documentation Status\n\n\nPython application that loads NCI-PID data into NDEx_\n\nThis tool downloads OWL_ files containing NCI-PID data from: ftp://ftp.ndexbio.org/NCI_PID_BIOPAX_2016-06-08-PC2v8-API/\nand performs the following operations:\n\n**1\\)** OWL files are converted to extended SIF_ format using Paxtools_ and the SIF_ file is loaded into a network\n\n**2\\)** A node attribute named **type** is added to each node and is set to one of the following\n   by extracting its value from **PARTICIPANT_TYPE** column in SIF_ file:\n\n* **protein** (originally ProteinReference)\n\n* **smallmolecule** (originally SmallMoleculeReference)\n\n* **proteinfamily** (set if node name has **family** and was a **protein**)\n\n* **RnaReference** (original value)\n\n* **ProteinReference;SmallMoleculeReference** (original value)\n\n**3\\)** A node attribute named **alias** is added to each node and is loaded from **UNIFICATION_XREF**\ncolumn in SIF_ file which is split by `;` into a list. Each element of this list is prefixed with **uniprot:** and t first element is set as the\n**represents** value in node and removed from the **alias** attribute. If after\nremoval, the **alias** attribute value is empty, it is removed.\n\n**4\\)** In SIF_ file **INTERACTION_TYPE** defines edge interaction type and **INTERACTION_PUBMED_ID** define\nvalue of **citation** edge attribute. The values in **citation** edge attribute are\nprefixed with **pubmed:** Once loaded redundant edges are removed\nfollowing these conventions:\n\n* **neighbor-of** edges are removed\n\n* **controls-state-of** edges are removed if another edge connecting same nodes has one of the following interactions: **controls-state-change-of, controls-transport-of, controls-phosphorylation-of, controls-expression-of**\n\n**NOTE:** If above results in orphaned nodes, those nodes are removed as well\n\n**5\\)** An edge attribute named **directed** is set to **True** if edge interaction type is one of the following (otherwise its set to **False**)\n\n.. code-block::\n\n    controls-state-change-of\n    controls-transport-of\n    controls-phosphorylation-of\n    controls-expression-of\n    catalysis-precedes\n    controls-production-of\n    controls-transport-of-chemical\n    chemical-affects\n    used-to-produce\n\n**6\\)** If node name matches **represents** value in node (with **uniprot:** prefix added) then the node name is replaced with gene symbol from `gene_symbol_mapping.json`_\n\n**7\\)** If node name starts with **CHEBI** then node name is replaced with value of **PARTICIPANT_NAME** from SIF_ column\n\n**8\\)** If node **represents** value starts with **chebi:CHEBI** the **chebi:** is removed\n\n**9\\)** If **_HUMAN** in SIF_ file **PARTICIPANT_NAME** column for a given node then this value is replaced by doing a lookup in `gene_symbol_mapping.json`_, unless value in lookup is **-** in which case original name is left\n\n**10\\)** Any node with **family** node name is changed as follows if a lookup of node name against **gene_symbol_mapping.json** returns one or more genes\n\n* Node attribute named **member** is added and set to list of genes found in lookup in `gene_symbol_mapping.json`_\n* Node attribute named **type** is changed to **proteinfamily**\n\n**11\\)** The following network attributes are set\n\n* **name** set to name of OWL_ file with **.owl.gz** suffix removed except for **PathwayCommons.8.NCI_PID.BIOPAX** which is renamed to **NCI PID - Complete Interactions**\n* **author** (from **Curated By** column in `networkattributes.tsv`_)\n* **labels** (from **PID** column in `networkattributes.tsv`_)\n* **organism** is pulled from **organism** attribute of `style.cx`_\n* **prov:wasGeneratedBy** is set to html link to this repo with text ndexncipidloader <VERSION> (example: ndexncipidloader 1.2.0)\n* **prov:wasDerivedFrom** is set to full path to OWL_ file on ftp site\n* **reviewers** (from **Reviewed By** column in `networkattributes.tsv`_)\n* **version** is set to Abbreviated month-year (example: MAY-2019)\n* **description** is pulled from **description** attribute of `style.cx`_ except for **NCI PID - Complete Interactions** which has a hardcoded description set to `This network includes all interactions of the individual NCI-PID pathways.`\n* **networkType** is set to list of string with single entry **pathway** except for **NCI PID - Complete Interactions** which also includes **interactome**\n* **__iconurl** is set to value of `--iconurl` flag (currently defaulting to http://search.ndexbio.org/static/media/ndex-logo.04d7bf44.svg)\n* **__normalizationversion** is set to 0.1\n\n**12\\)** By default each network is made public with full indexed and showcased (visible in user's home network list page)\n\nDependencies\n------------\n\n* `ndex2 <https://pypi.org/project/ndex2>`_\n* `ndexutil <https://pypi.org/project/ndexutil>`_\n* `biothings_client <https://pypi.org/project/biothings-client>`_\n* `requests <https://pypi.org/project/requests>`_\n* `pandas <https://pypi.org/project/pandas>`_\n\n\nCompatibility\n-------------\n\n* Python 3.3+\n\nInstallation\n------------\n\n.. code-block::\n\n   git clone https://github.com/ndexcontent/ndexncipidloader\n   cd ndexncipidloader\n   make dist\n   pip install dist/ndexncipidloader*whl\n\n\nConfiguration\n-------------\n\nThe **ndexloadncipid.py** requires a configuration file in the following format be created.\nThe default path for this configuration is :code:`~/.ndexutils.conf` but can be overridden with\n:code:`--conf` flag.\n\n**Format of configuration file**\n\n.. code-block::\n\n    [<value in --profile (default ndexncipidloader)>]\n\n    user = <NDEx username>\n    password = <NDEx password>\n    server = <NDEx server(omit http) ie public.ndexbio.org>\n\n\n**Example configuration file**\n\n.. code-block::\n\n    [ncipid_dev]\n\n    user = joe123\n    password = somepassword123\n    server = dev.ndexbio.org\n\n\nRequired external tool\n-----------------------\n\nPaxtools is needed to convert the OWL files to SIF format.\n\nPlease download **paxtools.jar** (http://www.biopax.org/Paxtools/) (requires Java 8+) and\nput in current working directory or specify path to **paxtools.jar** with `--paxtools` flag on\n**loadnexncipidloader.py**\n\nUsage\n-----\n\nFor more information invoke :code:`ndexloadncipid.py -h`\n\n**Example usage**\n\nThis example assumes a valid configuration file with paxtools.jar in the working directory.\n\n.. code-block::\n\n   ndexloadncipid.py sif\n\n**Example usage with sif files already downloaded**\n\nThis example assumes a valid configuration file and the SIF files are located in :code:`sif/` directory\n\n.. code-block::\n\n   ndexloadncipid.py --skipdownload sif\n\n\nVia Docker\n~~~~~~~~~~~~~~~~~~~~~~\n\n**Example usage**\n\nThis example **paxtools.jar** is in current directory, and a configuration\nfile has been created in current working directory and named :code:`conf`\n\n.. code-block::\n\n   docker run -v `pwd`:`pwd` -w `pwd` coleslawndex/ndexncipidloader:3.1.0 ndexloadncipid.py --paxtools `pwd`/paxtools.jar --conf conf sif\n\n\nCredits\n-------\n\nThis package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.\n\n.. _Cookiecutter: https://github.com/audreyr/cookiecutter\n.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage\n.. _NDEx: http://www.ndexbio.org\n.. _OWL: https://en.wikipedia.org/wiki/Web_Ontology_Language\n.. _Paxtools: https://www.biopax.org/Paxtools\n.. _SIF: https://bioconductor.org/packages/release/bioc/vignettes/paxtoolsr/inst/doc/using_paxtoolsr.html#extended-simple-interaction-format-sif-network\n.. _uniprot: https://www.uniprot.org/\n.. _gene_symbol_mapping.json: https://github.com/ndexcontent/ndexncipidloader/blob/master/ndexncipidloader/gene_symbol_mapping.json\n.. _networkattributes.tsv: https://github.com/ndexcontent/ndexncipidloader/blob/master/ndexncipidloader/networkattributes.tsv\n.. _style.cx: https://github.com/ndexcontent/ndexncipidloader/blob/master/ndexncipidloader/style.cx\n\n\n=======\nHistory\n=======\n\n3.1.0 (2019-09-11)\n-------------------\n\n* Added **--disableshowcase** flag that lets caller disable showcasing of **NEWLY** added networks which is enabled by default.\n\n* Added **--indexlevel** flag that lets caller set type of indexing performed on **NEWLY** added networks. Default is full indexing (all).\n\n3.0.0 (2019-08-02)\n-------------------\n\n* Renamed command line tool from **loadndexncipidloader.py** to **ndexloadncipid.py** to be more consistent with other loaders. Since this is a breaking change bumped to version 3.0.0\n\n* Added **--visibility** flag which lets caller dictate whether newly added networks are set to PUBLIC (default) or PRIVATE\n\n* Removed parameter **--disablcitededgemerge** since the changes in 2.0.0 causes this to no longer have any effect\n\n* Set default for **--paxtools** flag to be **paxtools.jar** which assumes the tool is in current working directory\n\n2.0.0 (2019-07-16)\n------------------\n\n* Spring layout adjusted by increasing iterations\n\n* Code now removes all neighbor-of edges with NO data migration. controls-state-change-of\n  edges are removed if more informative edges exist. Any orphaned nodes resulting from\n  the removal of these edges are also removed\n\n1.6.0 (2019-07-09)\n------------------\n\n* Added *__iconurl* network attribute to all networks\n\n* Added **interactome** to *networkType** network attribute for 'NCI PID - Complete Interactions' network\n\n1.5.1 (2019-07-09)\n------------------\n\n* Renamed network attribute *type* to *networkType* to adhere to normalization specification\n\n1.5.0 (2019-06-28)\n------------------\n\n* Fixed style.cx by removing view aspects that was causing networks to not render properly in cytoscape\n\n1.4.0 (2019-06-13)\n------------------\n\n* Network PathwayCommons.8.NCI_PID.BIOPAX is now renamed\n  to 'NCI PID - Complete Interactions' with alternate description.\n\n1.3.0 (2019-06-12)\n------------------\n\n* Improved description in style.cx file (JIRA ticket UD-362)\n\n1.2.0 (2019-06-11)\n------------------\n\n* Code now adds a citation attribute to every edge even if there is no value\n  in which case an empty list is set (JIRA ticket UD-360)\n\n* Added type network attribute and set it to ['pathway'] following normalization\n  guidelines\n\n1.1.0 (2019-06-10)\n------------------\n\n* Adjusted network layout to be more compact by reducing number of iterations in\n  spring layout algorithm as well as lowering the value of scale (JIRA ticket UD-360)\n\n1.0.2 (2019-05-24)\n------------------\n\n* Removed view references from cyVisualProperties aspect of style.cx file cause it was causing issues with loading in cytoscape\n\n* Set directed edge attribute type to boolean cause it was incorrectly defaulting to a string\n\n1.0.1 (2019-05-18)\n------------------\n\n* Renamed incorrect attribute name prov:wasDerivedBy to prov:wasDerivedFrom\n  to adhere to normalization document requirements\n\n1.0.0 (2019-05-16)\n------------------\n\n* Massive refactoring and first release where code attempts to behave as defined in README.rst\n\n0.1.1 (2019-02-15)\n------------------\n\n* Updated data/style.cx by renaming Protein to protein and SmallMolecule\n  to smallmolecule to match the new normalization conventions\n\n\n0.1.0 (2019-02-15)\n------------------\n\n* First release\n\n\n",
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