bioinformatics presentation to students university of minho

PROTOFILWWA computational platform for the analysis of the relationships between

microorganisms and environmental parameters in activated sludge plants

José Fernandes

Bioinformatics Master Thesis

Prof. Anália Lourenço

Prof. Ana Nicolau

System requirements

• Insertion and retrieval of data has to be done quickly and easily

• Should be possible to export the data so it can be analyzed with other informatics

systems

• Should support statistical assessments

• Have user-friendly visualization capabilities

• Controlled access to data, based on user roles, accounting for data privacy issues

• Easy dissemination of related studies and results

• Always online (web-based)

• Help finding additional information about the microorganisms present in the biological

samples

Overview of the workflow of field and lab work

PROTOFILWWPROTOFILWW

1.635 lines x 137 columns

ProtoFilWW system major components

1. Content Management component: supports the

researchers managing and analyzing the data obtained

from the WWTP’s samples

2. Text Mining component: finding additional information

about the microorganisms present in the biological

samples

High-level integration perspective of ProtoFilWW

Drupal core

PLUGINS

Import data

Reports Access control

Other services...

PROTOFILWW

SQL

XLS, TXT, CSV

Export dataXLS, TXT, CSV Solr/LuceneViews Solr Backend

Views

XML

Relational Database

UIMA

Contend Management component

• Open source Content Management System (CMS) and

Framework (CMF)

• Highly modular and with high extensibility

• Built in the PHP scripting language

WWTP Sample

1. Filamentous bacteria

2. Protozoa

3. Metazoa

4. Physical-chemical

5. Sample characterization

User roles

use case visitors collaborators WWTP researchers administrators

Find studies and results x x x x

Contact researchers x x x

Analysis of available data x

Data insertion x x

Creation of reports x

Export data x

Managing users x

Backup data x

Text Mining x x x x

Dynamic reporting and charting

Reports creation Reports display

Geolocation of the WWTPs

Address geocoding Map display

Text Mining

componentListing the species

mentioned in a

document

Major Text Mining technologies used

• Lucene is a high-performance text search engine

library.

• Solr is a standalone enterprise search server with a

REST-like API

• UIMA is a powerful infrastructure for the storage,

transport, and retrieval of document and annotation

knowledge accumulated in NLP pipeline systems

• LINNAEUS is a popular organism name identification

system for biomedical literature that is capable of

normalizing to unambiguous NCBI taxonomy identifiers

Text Mining process in ProtoFilWW

Solr/Lucene

LINNAEUS

Solr UIMA

PMC Open Access SubsetPMC Open Access Subset Solr XML documentsSolr XML documents

XPath convertion

Solr LINNAEUS Annotator

UIMA Component Descriptor Editor plugin

UIMA type system for LINNAEUS

LINNAEUS UIMA wrapper running on CVD

Drupal Views Solr Backend

Major contributions

1. The Web-based computational system

www.protofilww.org

2. The Drupal module Views Solr Backend

3. The Solr UIMA plug-in for LINNAEUS Annotator

Em que trabalho após o mestrado…

Preventive Medicine

Alert the user to the risk of Type 2 Diabetes.

How?

1. We know the user has a gene mutation associated with Type 2

Diabetes, because he gave us is genome!

2. We know what he has eaten, because he told us!

3. We know what exercise he’s been doing, because he told us!

4. Genehome connects the dots!