An open-source medical search engine
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docker
retrieval_and_indexing
solr_configuration
www
LICENSE
README.md

README.md

FindMeEvidence

An open-source medical search engine

Install Solr

  1. Download Apache Tomcat and Apache Solr 4.X

  2. Copy example/solr to your SOLR_HOME and replace solrconfig.xml, schema.xml and synonyms.txt from collection1

  3. Copy solr_configuration/solr.xml to CATALINA_HOME/conf/Catalina/localhost (point to your SOLR_HOME and Solr WebApp)

  4. Copy all jars from example/lib/ext into your container's main lib directory (CATALINA_HOME/lib)

  5. Copy solr_configuration/collection2 to SOLR_HOME/solr and use the Core Admin to add the core

Create Solr Index

The folder retrieval_and_indexing contains scripts for fetching external content, indexing it in Solr, as well as creating synonym mappings. The scripts should be called from the command line (e.g., with a command such as "php start_crawl.php"). Prior to running the scripts, please ensure that the CURL & SQLite modules and a JAVA JRE are installed (in Ubuntu simply do a sudo apt-get install php5-curl php5-sqlite openjdk-8-jre).

###Preparatory Work

Define constants SOLR_URL and SOLR_URL_DIC in config.php to point to the Solr cores.

###Fetching and indexing PubMed

  1. optional

    • Run pubmed_oa_fetch.php to fetch OA article IDs from the PMC OA Web Service

    • Run pubmed_oa_remove_duplicates.php to remove duplicate IDs

    • Run pubmed_oa_insert_into_db.php to insert all IDs in a SQLite3 DB

  2. Run pubmed_fetch.php: pubmed_fetch.php downloads all PubMed entries that are the result of a specific PubMed query. You can edit the script to change the PubMed query used. The default query aims to cover all content in PubMed that is of relevance for medical decision making.

  3. Run pubmed_xml_to_solr_xml.php: pubmed_xml_to_solr_xml.php iterates through the PubMed XML files downloaded by pubmed_fetch.php, reads PubMed entries, and writes extracted content to the Solr index.

###Fetching and indexing Wikipedia

  1. optional (get a free API key and store it in the property file config.php)

    • If a new list of MeSH Descriptors (preferred terms only) is available at http://www.nlm.nih.gov/mesh/filelist.html download the list to the wikipedia folder an run generate_new_english_terms.sh mshd20XX.txt

    • Run wikipedia_create_list_of_relevant_articles.php

    • Run wikipedia_remove_duplicates.php to remove duplicate IDs

    • Run wikipedia_langlinks_translate_de.php to use the Wikipedia langlink as the german translation of the article

    • Run wikipedia_translate_de.php to translate the remaining article titles with Yandex to german (Powered by Yandex.Translate)

    • Run wikipedia_translate_de.php again if translation was reached

    • Run wikipedia_langlinks_translate_es.php to use the Wikipedia langlink as the spanish translation of the article

    • Run wikipedia_translate_es.php to translate the remaining article titles with Yandex to spanish (Powered by Yandex.Translate)

    • Run wikipedia_translate_es.php again if translation was reached

  2. Run wikipedia_fetch.php to download articles from Wikipedia

  3. Run wikipedia_xml_to_solr_xml.php: wikipedia_xml_to_solr_xml.php iterates through the Wikipedia XML files downloaded by wikipedia_fetch.php, reads Wikipedia entries, and writes extracted content to the Solr index.

  4. Run wikipedia_translations_to_solr_xml.php: wikipedia_translations_to_solr_xml.php indexes the translations to the dictionary Solr core

###Crawling and indexing websites

  1. Run start_crawl.php

###Creating synonyms from Wikipedia

  1. Run create_synonyms_from_wikipedia.php: This creates a synonym mapping (for improving quality of search results) based on page redirects in Wikipedia. To do this, it calls the DBpedia server (an open database where content from Wikipedia can be queried). The script writes synonyms to a file in the ./synonyms subfolder. This file must be placed into the Solr directory of the Solr collection containing the index., e.g., as [SOLR_HOME]/collection1/conf/synonyms.txt.

###Cleaning the index

  1. Run clean_index.php: This simple script removes document from the index that match a certain Solr query. Can be used to clean up unwanted stuff that slipped through in earlier indexing steps.

Log to a Log File

Set the log level and the name of the file to write to in www/logger_config.xml.