OpenAIRE-COAR conference 2014: Argo - a platform for interoperable and customisable text analytics,...

Argo: a platform for interoperable and customisable text mining

Sophia Ananiadou National Centre for Text Mining

School of Computer Science

The University of Manchester

Overview

• Sharing tools, resources and text mining workflows

• Challenges

• Interoperable infrastructure for processing and annotation

2 Open AIRE-COAR Conference Ananiadou

NaCTeM

• 1st publicly funded national text mining centre

• Location: Manchester Institute of Biotechnology

• Phase I - Biology (2004-2008)

• Phase II - Biology, Medicine, Social Sciences (2008-2011)

• Phase III – Biology, Medicine, Humanities, Social Sciences; Fully sustainable centre (2011-)

www.nactem.ac.uk

Challenges

Language Technology

Languages English French German Spanish Portuguese Italian Polish …. Chinese Hindu Urdu Japanese Korean…. Tasks

Translation Information Extraction Semantic Search Question Answering Sentiment Analysis Summarization Knowledge Discovery

….

Domains Finance/Business Health Biology Social Sciences Humanities….

Text Types Newswire Scientific Literature Full papers/abstracts Twitter Patents Clinical records, EMR Textbooks, monographs Online forums….

Technology Sentence Splitter Paragraph Splitter NP Chunkers C-parser D-parser Semantic parser NE recognizers Relation recognizers …….

Diversity of Languages

Diversity of Contexts

Diversity of Applications

TM Workflows

TM Modules

Shared!


Metadata Languages English French German Spanish Portuguese Italian Polish …. Chinese Hindu Urdu Japanese Korean… Tasks

Translation Information Extraction Semantic Search Question Answering Sentiment Analysis Summarization Knowledge Discovery

….

Language Technology

Linguistic Resources Knowledge Resources

Resource-Rich

Big Data Big Text

Cloud Computing Crowd Sourcing

Big Ontology

Text Types Newswire Scientific Literature Full papers/abstracts Twitter Patents Clinical records, EMR Textbooks, monographs Online forums….

Domains Finance/Business Health Biology Social Sciences Humanities….


OPEN SCIENCE

Requirements from TM infrastructure

• Modularity of TM modules

• Interoperability among TM modules and resources

• Generic across different languages, domains, and text types

– Adaptability


Module

Interoperability and Adaptability

Module

Module

Resources Dictionaries Ontologies

Adaptation

Rule Writing

(Annotated) Text

Interoperability and Adaptability in Resource-rich TM INFRASTRUCTURES!

Dependency Parser

English French German Japanese Greek

POS Tagger Named Entity Languages

Text Types Domains


Example: extracting proteins, annotations

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GENIA

PennBioIE

AIMed

GENETAG

Incompatibility

Type definitions Texts

Problem: Inconsistency

Open AIRE-COAR Conference Ananiadou

The problem with incompatibility

• Difficult to evaluate NERs

9 Corpus C Corpus D

NER A

Which NER is best for my

task?

NER B

A: 93% B: 36% A is better than B.

A: 63% B: 90% B is better than A.

Why so different among different corpora and

NERs ?

Open AIRE-COAR Conference Ananiadou

Text mining workflows

• A pipeline that executes particular tools and resources in order

• Example: semantic search

• Various versions (language- or domain-specific) of basic components needed for different applications and tasks

• Different workflows can be created, compared and evaluated by the ability to seamlessly “mix and match” various versions of components

PoS Tagger

Dictionary Lookup

NE Extraction

Chunking Parsing Semantic

Query


Text mining workflows

Interoperability

Common Data Representation and Types

IBM Journal of Research and Development (2011)

U-Compare: a modular NLP workflow construction and evaluation system.

Kano, Y., Miwa, M., Cohen, K. B., Hunter, L., Ananiadou, S. and Tsujii, J.


Common Type System

• A common type system is required for the complete interoperability

• Solution: Maintain local type systems and bridge them via a sharable type system

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A single common type is almost impossible to impose

for all developers.

U-Compare

Sharable Type System Local Type System A Local Type System B

bridging bridging


U-Compare Type System

Syntactic Level

Document Level

Semantic Level


POS tagger B

Sentence Splitter B

library

POS tagger A

Sentence Splitter A

NER

Sentence Splitter A Sentence Splitter A Sentence Splitter A

Sentence Splitter B Sentence Splitter B Sentence Splitter B

POS tagger A

POS tagger A

POS tagger A

POS tagger B

POS tagger B

POS tagger B

NER NER NER

Workflow A Workflow B Workflow C

F-Score A F-Score B F-Score C

U-Compare: Evaluate and Compare TM Worklfows

UIMA SD

OpenNLP SD

GENIA SD

UIMA Tokenizer

OpenNLP Tokenizer

GENIA Tagger as Tokenizer

GENIA Tagger

Stepp Tagger

OpenNLP Tagger

ABNER

MedT-NER

GENIA Tagger as NER

• Web-based application

• Interactive creation of workflows

• Cloud and high-performance computing

• Integrated TM/NLP processing system • GUI for workflow creation • Library of ready-to-use processing components • Statistics, visualizations, developer APIs • Supports UIMA • http://argo.nactem.ac.uk

15

Database: The Journal of Biological Databases and Curation (2012)

Argo: an integrative, interactive, text mining-based workbench supporting curation.

Rak, R., Rowley, A., Black, W.J. and Ananiadou, S

http://argo.nactem.ac.uk

http://argo.nactem.ac.uk

Structured Data

Remote Processing

Workflow Diagramming

Workflow Designer

Manual Editing

Annotator/Curator

Processing Components

Developers

UIMA Compliance

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Processing Components

• Approaching 100 components (U-Compare)

– Additional 50 will be added soon

• META-NET

• Developed or co-developed by NaCTeM

– Planned: Make the library open to others to contribute

• Generic Listener component

– Developers can plug in their own locally run UIMA component to a workflow in Argo


Remote Processing

• Single machine execution

– In-house high-performance machines

• Distributed processing

– HTCondor

– VMware vCloud (EBI) EUPMC

– Planned: EC2, Azure, …


Workflows

• Users create workflows as block diagrams

• Workflows can be shared among users

– Read only

– Planned: Read & write

– Planned: downloadable workflows

• Workflows can be deployed as web services

– Plain text (input only), XMI, RDF, BioC


Workflows view


Workflow Editor

21 Open AIRE-COAR Conference

Sample Use Cases

1 Recognition of chemical entities (chemical NER)

2 Semi-automatic curation of metabolic pathways

3 Evaluation of inter-annotator agreement

4 Information extraction as a Web service

Ananiadou Open AIRE-COAR Conference 22

Use Case 1: Chemical NER

Supplies gold standard corpus

Removes golden annotations so that they can be created

automatically

Combinations of syntactic and semantic components create

annotations

Compares and reports precision, recall and F1 of the different branches against the gold standard corpus

Chemical Entity Recogniser

• Chemical model evaluated at BioCreative IV CHEMDNER challenge

• The challenge

– Data: 10,000 manually annotated PubMed abstracts

– Automatically recognises names of chemical entities in text


Chemical Entity Recogniser

• Our solution

– Ranked unique mentions: ranked 1st out of 18 groups

– All mentions: ranked 3rd out of 19 groups

Subtask Precision % Recall % F-score %

Ranked unique mentions 91 85 88

All mentions 93 81 87


Use Case 2: Semi-automatic Curation – Metabolic Pathways

Search for relevant

documents

Manual correction of automatic annotations

NER for chemicals, genes, process

indicators

Linking to ontologies: CTD, ChEBI, UniProt


Save results in various formats,

e.g., RDF for querying and

incorporation into databases

Manual Annotation Editor

Create new annotations by selecting text

Create, modify or delete annotations

Edit details of annotations

Open a graphical interface to link annotations to

ontologies


Filtering and converting annotations


Manual Annotation Editor: linking to ontologies Automatic pre-

selection can be modified by the user

Details show ontology entry

webpage


Use Case 3: Information extraction as a Web service

Web service-enabled reader

Web service-enabled writer


Language Universal

• Reusable modules

• Generic TM modules: Competence

• Annotated Text, corpora: Performance

• Standards of Data Representation and Types for Resources: Competence

• Dictionaries, Thesauri, Ontologies: Performance


Date post:	26-Jan-2015
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