=============== AnnotationPress

Overview

AnnotationPress is designed to provide a user friendly tool that helps scientists annotate scientific claims, data, and evidence in HTML and PDF documents. The current version is configured to annotated drug-drug interactions in both full text journal articles and structured product labeling. This is a particularly challenging domain that required the development of several annotation workflows which we think will be useful for for other scientific domains. A key aspect of AnnotationPress is its use of annotation plug-ins which make the tool is easily adaptable to other annotation use cases. Another distinctive feature is that AnnotationPress implements the Micropublication <https://jbiomedsem.biomedcentral.com/articles/10.1186/2041-1480-5-28> and Open Annotation data <http://www.openannotation.org/spec/core/> standards. These standards specify how to relate annotations in target documents about data, methods, and materials to scientific claims.

If you are new to AnnotationPress, please watch our video <https://goo.gl/kF1aaM>_ that show two annotation plugins in action.

AnnotationPress is an Apache licensed open source project available on github <https://github.com/dbmi-pitt/dbmi-annotator>_. Please contact us if you are interested in contributing to its development, if you would like to request new features, or have any other questions.

Licensing

AnnotationPress is licensed under the Apache License, Version 2.0. See LICENSE for the full license text.

How to run - Production

(1) Install docker(v1.12.3), docker-compose (v1.8.1) and apache (v2.4) server

Apache2 server configuration

.. code-block::

# AnnotationPress Docker configuration ###############################

# proxy for docker exposed service at port 8085

ProxyPass /dbmiannotator http://localhost:8085/dbmiannotator
RewriteRule /dbmiannotator(.*) http://localhost:8085/dbmiannotator$1 [P]

# proxy for docker exposed service at port 8085 for annotator store

ProxyPass /annotatorstore http://localhost:8085/annotatorstore
RewriteRule /annotatorstore(.*) http://localhost:8085/annotatorstore$1 [P]

# stylesheet folder relocate at Document root(dailymed, PMC, wiley)

RewriteRule /dbmiannotator/dailymed(.*) http://localhost/DDI-labels/dailymed$1 [P]
RewriteRule /dbmiannotator/PMC(.*)_files/(.*) http://localhost/PMC/PMC$1_files/$2 [P]
RewriteRule /dbmiannotator/wiley(.*)_files/(.*) http://localhost/wiley/wiley$1_files/$2 [P]

(2) Create local volume for postgres and elasticsearch data mount point::

$ docker volume create --name postgres-volume -d local
$ docker volume create --name elasticsearch-volume -d local
$ docker volume create --name elastic-snapshot-volume -d local

(3) Run dbmi-annotator with all dependencies in docker container::

$ git clone 
$ cd docker-dbmi-annotator/dbmi-annotator
$ docker-compose up

Optional: pre-load annotations from csv to DB mpevidence

$ python loadDomeoAnnsToRDB.py <pghostname> <pgport> <pguser> <pgpassword> <clean existing data (1: yes, 0: no)>

ex. $ python loadDomeoAnnsToRDB.py postgres 5432 dbmiannotator dbmi2016 1

1. optional: clean all data in table
2. preprocess csv, generate preprocess-domeo.csv
3. load data into schema mpevidence

Optional: pre-load annotations from postgres DB mpevidence to elasticsearch

$ docker exec -it dbmi-annotator bash
$ cd translation/rdb-data-loader
$ python load-rdb-annotations.py <pg hostname> <pg username> <pg password> <es hostname> <annotation author>

ex. python load-rdb-annotations.py postgres dbmiannotator dbmi2016 elasticsearch test@gmail.com

For how to build production mode via docker: https://github.com/dbmi-pitt/docker-dbmi-annotator/blob/master/README

How to run - Development

Dependences: ^^^^^^^^^^^^

1. Elasticsearch version 1.7 running on port 9200

2. Annotator Store running on port 5000

3. Postgres DB running on port 5432:

   create database dbmiannotator

   SQL script that create dbmiannotator schema: https://github.com/dbmi-pitt/dbmi-annotator/blob/master/db-schema/rdb-postgres-schema.sql

   SQL script that initialize plugin settings: https://github.com/dbmi-pitt/dbmi-annotator/blob/master/db-schema/rdb-postgres-initial.sql

4. Apache2 server running on port 80

Installation: ^^^^^^^^^^^^^

1. nodejs packages $ npm install

2. compile browser side JS packages (rerun when made modifications on config/config.js) $ browserify app.js -o public/dbmiannotator/js/app.bundle.js

Configuration: ^^^^^^^^^^^^^^

1.Create config.js $ cp config/config.sample.js config/config.js

2.Edit config.js based on system environment

3.Apache2 configurations:

.. code-block::

#proxy for local nodejs server on port 3000
RewriteRule /dbmiannotator$ http://localhost:3000/dbmiannotator [P]
RewriteRule /dbmiannotator/(.*) http://localhost:3000/dbmiannotator/$1 [P]

#proxy for local annotator store on port 5000
ProxyPass /annotatorstore http://localhost:5000/
RewriteRule /annotatorstore(.*) http://localhost:5000$1 [P]  

Run server: ^^^^^^^^^^ .. code-block::

$ cd dbmi-annotator
$ nodemon server.js (run '$ npm install -g nodemon', if command is not available)
$ service apache2 start

access AnnotationPress through ``'http://localhost/dbmiannotator'``

Add documents to annotate: ^^^^^^^^^^ 1) Download the HTML using your browser to some place e.g., /path/

2) If needed, rename the file to a more appropriate name. E.g., for PMC articles, it is good to concatenate 'PMC' with the article's PMC identifier. For example, for PMC 1459289 you would:

$ mv /path/file.html /path/PMC1459289.html

$ mv /path/file_files /path/PMC1459289_files

3) Add html document and related files to apache2 home directory that is relevant for the papers publisher. E.g., for PMC:

$ cp -r /path/PMC1459289* /var/www/html/PMC/

4) Register new document by opening up in a text editor the relevant file in the folder dbmi-annotator/article-list/ . For example, for PMC:

$ sublime article-list pmc-list.csv