reactome / content-service

The new Reactome REST API to access the data

Reactome Content Service

What is the Reactome Content Service

The Content Service is the Reactome API to access the data. It is based on Spring MVC, based on REST and fully documented in Open API (previously Swagger). Through the ContentService API you'll have access to the Graph Database, Interactors and SolR Search.

Installation Guide

• ⚠️ Pre-Requirement (in the given order)
  1. Maven 3.X - Installation Guide
  2. Reactome Graph Database - Installation Guide
  3. Interactor Database - Installation Guide
  4. Search SolR Index - search-indexer
  5. Mail Server (if you don't have a valid SMTP Server, please refer to FakeSMTP

Git Clone

git clone https://github.com/reactome/content-service.git
cd content-service

Configuring Maven Profile 📝

Maven Profile is a set of configuration values which can be used to set or override default values of Maven build. Using a build profile, you can customize build for different environments such as Production v/s Development environments. Add the following code-snippet containing all the Reactome properties inside the tag <profiles> into your ~/.m2/settings.xml. Please refer to Maven Profile Guideline if you don't have settings.xml

<profile>
    <id>reactome</id>
    <properties>
        <mail.host>localhost</mail.host>
        <mail.port>8181</mail.port>
        <mail.username>username</mail.username>
        <mail.password>password</mail.password>
        <mail.enable.auth>true</mail.enable.auth>

        <!-- Neo4J Configuration -->
        <neo4j.uri>bolt://localhost:7687</neo4j.uri>
        <neo4j.user>neo4j</neo4j.user>
        <neo4j.password>password</neo4j.password>

        <!-- Solr Configuration -->
        <solr.host>http://localhost:8983/solr</solr.host>
        <solr.core>reactome</solr.core>
        <solr.user>admin</solr.user>
        <solr.password>password</solr.password>

        <!-- MySQL Configuration -->
        <mysql.host>localhost</mysql.host>
        <mysql.port>3306</mysql.port>
        <mysql.reactome.database>reactome</mysql.reactome.database>
        <mysql.report.database>report</mysql.report.database>
        <mysql.user>curator</mysql.user>
        <mysql.password>password</mysql.password>

        <template.server>https://localhost/</template.server>

        <!-- Log report -->
        <cnf.mail.error.subject>Automated Error Report</cnf.mail.error.subject>
        <cnf.mail.error.name>Error Report Agent</cnf.mail.error.name>
        <cnf.mail.error.from>[email protected]</cnf.mail.error.from>
        <cnf.mail.error.to>[email protected]</cnf.mail.error.to>

        <!-- Report mail Configuration -->
        <cnf.mail.report.hostname>reactome.org</cnf.mail.report.hostname>
        <cnf.mail.report.from>[email protected]</cnf.mail.report.from>
        <cnf.mail.report.to>[email protected]</cnf.mail.report.to>

        <!-- Results not found internal Report -->
        <report.user>reportadmin</report.user>
        <report.password>password</report.password>

        <!-- Logging -->
        <logging.level>ERROR</logging.level>
        <logging.dir>/var/log/tomcat7</logging.dir>

        <!-- Analysis intermediate file  -->
        <analysis.structure.file>/usr/local/reactomes/Reactome/production/AnalysisService/input/analysis.bin</analysis.structure.file>
        <analysis.result.root>/usr/local/reactomes/Reactome/production/AnalysisService/temp</analysis.result.root>

        <!-- Common folders and file locations -->
        <fireworks.json.folder>/usr/local/reactomes/Reactome/production/Website/static/download/current/fireworks</fireworks.json.folder>
        <diagram.json.folder>/usr/local/reactomes/Reactome/production/Website/static/download/current/diagram</diagram.json.folder>
        <diagram.exporter.temp.folder>/usr/local/reactomes/Reactome/production/ContentService/exporter/</diagram.exporter.temp.folder>
        <tuples.uploaded.files.folder>/usr/local/reactomes/Reactome/production/ContentService/custom</tuples.uploaded.files.folder>

        <!-- Needed for the Content-Service / Raster exporter -->
        <ehld.folder>/usr/local/reactomes/Reactome/production/Website/static/download/current/ehld</ehld.folder>
        <svg.summary.file>/usr/local/reactomes/Reactome/production/Website/static/download/current/ehld/svgsummary.txt</svg.summary.file>

        <!-- Path to the experiments binary file -->
        <experiments.data.file>/usr/local/reactomes/Reactome/production/AnalysisService/digester/experiments.bin</experiments.data.file>
    </properties>
</profile>

Running ContentService activating reactome profile.

mvn spring-boot:run -P reactome

Check if Tomcat has been initialised

[INFO] Using existing Tomcat server configuration at /Users/reactome/content-service/target/tomcat
INFO: Starting ProtocolHandler ["http-bio-8686"]

Usage

• 💻 Access your local installation

content-service's Issues

How to convert .sbgn glyph ids to protein Identifiers

I downloaded the SBGN file for pathway R-HSA-400511 from the reactome website. Is there anyway that I can convert the glyph id to there associated protein or compound id?

....
 <glyph class="process" id="reactionVertex_400459_16">
            <label text="Signal peptidase hydrolyzes preproGLP-1 to proGLP-1"/>
            <bbox w="12.0" h="12.0" x="316.0" y="297.0"/>
            <port id="reactionVertex_400459.1" x="321.0" y="313.0"/>
            <port id="reactionVertex_400459.2" x="322.0" y="293.0"/>
        </glyph>
        <glyph class="simple chemical" id="entityVertex_70115_38">
            <label text="Glc"/>
            <bbox w="35.0" h="30.0" x="18.0" y="878.0"/>
        </glyph>
        <glyph class="complex" id="entityVertex_264960_18">
            <label text="Signal Peptidase"/>
            <bbox w="125.0" h="24.0" x="459.0" y="244.0"/>
        </glyph>
        <glyph class="omitted process" id="reactionVertex_400509_42">
            <label text="Glucose-dependent Insulinotropic Polypeptide is secreted from intestinal K cells"/>
            <bbox w="12.0" h="12.0" x="762.0" y="780.0"/>
            <port id="reactionVertex_400509.1" x="767.0" y="796.0"/>
            <port id="reactionVertex_400509.2" x="768.0" y="776.0"/>
        </glyph>
....

pathwayCommons offers a mapping table with each glyph id and their associated uniprot id. Is there anything like this for Reactome?

 Uniprot                                                                     pathwayCommons
1  325053920   http://pathwaycommons.org/pc12/Protein_intact_EBI-8580945_identity_1568340696910
2 A0A024QZJ7 http://pathwaycommons.org/pc12/Protein_uniprotkb_A0A024QZJ7_identity_1568341662043
3 A0A024QZJ7 http://pathwaycommons.org/pc12/Protein_uniprotkb_A0A024QZJ7_identity_1568341663929
4 A0A024QZN9 http://pathwaycommons.org/pc12/Protein_uniprotkb_A0A024QZN9_identity_1568341660942
5 A0A024QZN9 http://pathwaycommons.org/pc12/Protein_uniprotkb_A0A024QZN9_identity_1568341663069
6 A0A024QZR3 http://pathwaycommons.org/pc12/Protein_uniprotkb_A0A024QZR3_identity_1568341661337

/WEB-INF/pages/header.jsp not found

run

mvn tomcat7:run -D... 

then view on browser: http://localhost:8686, there throws out en exception:

javax.servlet.ServletException: File "/WEB-INF/pages/header.jsp" not found

there's no header.jsp in WEB-INF dir, is the file missing?