Welcome to the FAQ section

• How is the score is calculated ?
  The score is calculated as the p-value of a chi-squared test. This is based on co-occurrence of markers and diseases within abstracts or sentences. For each marker/disease pair, a 2x2 contengency table is built, containing the entries true positives, true negatives, false positives, and false negatives.
  
  ● True positives are defined as the number of co-occurences of a specific marker and disease pair.
  
  ● False negatives are defined as the amount of matches for the marker that do not contain the specific disease.
  
  ● False positives are defined as the amount of matches for the disease that do not contain the specific marker.
  
  ● True negatives are defined as the amount of all other matches that do not contain the specific disease and marker.
  
  The chi-squared test checks if a marker/disease pair has more co-occurences than expected just by chance. The lower the score, the higher ist he reliability of the specific marker/disease pair.
• What is the defintion of sentence-wise search option?
  Sentence-wise means that biomarker and disease has to in one sentence, to be found as a pair.
• What are the datasources?
  Free PubMed abstracts, that are labelled with the MeSH Term "biomarker" or "biological marker", are processed with text-mining methods to find marker-diseases pairs. Sources for diseases and potential biomarkers are Disease Ontolog, the UniProt gene/protein database and mirBase .
• How does the text mining work?
  BIONDA uses the Named Entity Recognition (NER) approach from text mining. NER distinguishes between rule based, machine learning and dictionary based approaches. BIONDA currently uses the dictionary based approach. One requirement is to have good data sources, which BIONDA obtains from UniProt, Disease Ontology, PubMed and mirBase. The tool compares the preprocessed abstracts with a database of diseases and markers and saves the matches in BIONDA.
• What is a PMID?
  Every PubMed abstract has a PMID number. It is a unique eight-digit number, which allows to indetifer the abstract.
• How can I use the advanced search?
  To use the advanced search you can use the navigation on the main page or in the header. Details on the use oft he advanced search are explained in the following page.
  
• How can I contact the BIONDA team?
  You can reach us via the contact details on the Contact page.

• How can I evaluate BIONDA?
  Please use the contribute form to evaluate BIONDA. The evaluation takes place via a de.NBI survey, which can also be accessed from here.
• I want to contribute !
  Please use the contribute page. to mark wrong entries, add new entries or curate entres. A tutorial can be found here.