Add identifiers to all FamPlex entries

.gitignore

@@ -0,0 +1,101 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# IPython Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# dotenv
+.env
+
+# virtualenv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+
+# Rope project settings
+.ropeproject
+
+# PyCharm project settings
+.idea/*
+
+*.pickle
+*.gpickle
+
+scratch
+scratch/*
+
+.pytest_cache
+.DS_Store

.travis.yml

@@ -4,25 +4,21 @@ python:
 before_install:
   - sudo apt-get install graphviz
   - pwd
-  - pip install future requests pygraphviz
-  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
-      pip install functools32;
-    fi
+  - pip install future requests pygraphviz bel_resources
   - git clone https://github.com/sorgerlab/indra.git
 script:
   - pwd
   - echo $TRAVIS_BUILD_DIR
   - export PYTHONPATH=$PYTHONPATH:$TRAVIS_BUILD_DIR/indra
-  - python check_references.py
-  - python export/relations_graph.py
+  - python famplex/check_references.py
+  - python famplex/export/export_relations_graph.py
   # test if exports have been updated
   # bel_resources must be installed to generate belns exports
   # generate exports then take git diff and look only at lines that changed
   # lines containing date, timestamp, or version should be ignored
-  - pip install bel_resources
-  - python export/obo.py
-  - python export/hgnc_ids.py
-  - python export/belns.py
+  - python famplex/export/export_obo.py
+  - python famplex/export/hgnc_ids.py
+  - python famplex/export/export_belns.py
   - export belns_diff=$(git diff -U0 export/famplex.belns | egrep "^[\+-][^\+-]")
   - export belns=$(echo "$belns_diff" | egrep -v "^[\+-](VersionString|CreatedDateTime)")
   - export obo_diff=$(git diff -U0 export/famplex.obo | egrep "^[\+-][^\+-]")

README.md

@@ -31,6 +31,10 @@ the FamPlex namespace.
 
 * ```entities.csv```. A registry of the families and complexes defined in the
   FamPlex namespace.
+
+* ```descriptions.csv```. Descriptions and citations of some entities. Contains
+  three columns: the FamPlex name, comma separated reference CURIEs, and a 
+  textual description.
 
 * ```grounding_map.csv```. Explicit mapping of text strings to identifiers in
   biological databases.
@@ -61,7 +65,7 @@ relationships, including sub-families (families within families) and complexes
 consisting of families of related subunits (e.g., PI3K, NF-kB).
 
 The ```relations.csv``` file consists of five columns: (1) the namespace for
-the subject (e.g., ```HGNC``` for gene names, ```UP``` for Uniprot, or
+the subject (e.g., ```HGNC``` for gene names, ```UP``` for UniProt, or
 ```FPLX``` for the FamPlex namespace), (2) the identifier for the subject,
 (3) the relationship (```isa``` or ```partof```), (4) the namespace for the
 object, and (5) the identifier for the object.
@@ -87,10 +91,10 @@ cancer.
 
 Entities are grounded to the following databases:
 
-* Genes/proteins: [Uniprot](http://www.uniprot.org)
+* Genes/proteins: [UniProt](http://www.uniprot.org)
 
 * Chemicals: [PubChem](https://pubchem.ncbi.nlm.nih.gov/),
-  [CHEBI](https://www.ebi.ac.uk/chebi/), and [HMDB](http://www.hmdb.ca/) (for
+  [ChEBI](https://www.ebi.ac.uk/chebi/), and [HMDB](http://www.hmdb.ca/) (for
   metabolites)
 
 * Biological processes: [GO](http://geneontology.org/) and
@@ -99,7 +103,7 @@ Entities are grounded to the following databases:
 * Protein families and named complexes: grounded to entities defined within
   the FamPlex repository in the ```entities.csv``` and ```relations.csv```
   files, and to identifiers in [PFAM](http://pfam.xfam.org/)
-  and [Interpro](https://www.ebi.ac.uk/interpro/) when possible.
+  and [InterPro](https://www.ebi.ac.uk/interpro/) when possible.
 
 ## Gene prefixes