The pragmatic text miner: It’s just another type of poorly standardized data

•Download as PPT, PDF•

0 likes•644 views

This document discusses text mining and challenges working with unstructured biomedical data from various sources. It describes using named entity recognition, expansion rules, and co-mentioning within texts to identify related entities. Integrating text mining with curated knowledge bases and other data can provide more insights but requires common identifiers and dealing with different formats, licenses, and qualities of information from multiple sources. Collaboration is important to make the most of technology and domain expertise.

Lars Juhl Jensen
The pragmatic text miner
It’s just another type of poorly standardized
data

Acknowledgments
Protein networks
Michael Kuhn
Damian Szklarczyk
Andrea Franceschini
Milan Simonovic
Alexander Roth
Sune Pletscher-
Frankild
Jianyi Lin
Pablo Minguez
Christian von Mering
Peer Bork
Localization and disease
Sune Pletscher-Frankild
Alberto Santos
Janos Binder
Kalliopi Tsafou
Christian Stolte
Albert Palleja
Heiko Horn
Evangelos Pafilis
Reinhardt Schneider
Sean O’ Donoghue

What's hot

The STRING database and related tools

Lars Juhl Jensen

The STRING database

Lars Juhl Jensen

Network biology: A crash course on STRING and Cytoscape

Lars Juhl Jensen

STRING - Large-scale integration of data and text

Lars Juhl Jensen

STRING/STITCH tutorial

biocs

Turning big data and text collections into web resroucesLars Juhl Jensen

Text mining for organism and environment names

Lars Juhl Jensen

The STRING database

Lars Juhl Jensen

Data integration with STRINGLars Juhl Jensen

Gene association networks - Large-scale integration of data and text

Lars Juhl Jensen

Network biology: Large-scale data and text mining

Lars Juhl Jensen

Network biology: Large-scale data integration and text miningLars Juhl Jensen

Biomarker bioinformatics: Network-based candidate prioritization

Lars Juhl Jensen

Gene association networks: Large-scale integration of data and text

Lars Juhl Jensen

Gene association networks: Large-scale integration of data and text

Lars Juhl Jensen

Scientific Highlights: The Reflect and NetPhorest web resources

Lars Juhl Jensen

Networks of proteins and diseasesLars Juhl Jensen

Gene association networks - Large-scale integration of data and text

Lars Juhl Jensen

Large-scale integration of data and text

Lars Juhl Jensen

Protein association networks: Large-scale integration of data and text

Lars Juhl Jensen

What's hot (20)

The STRING database and related tools

The STRING database

Network biology: A crash course on STRING and Cytoscape

STRING - Large-scale integration of data and text

STRING/STITCH tutorial

Turning big data and text collections into web resrouces

Text mining for organism and environment names

The STRING database

Data integration with STRING

Gene association networks - Large-scale integration of data and text

Network biology: Large-scale data and text mining

Network biology: Large-scale data integration and text mining

Biomarker bioinformatics: Network-based candidate prioritization

Gene association networks: Large-scale integration of data and text

Scientific Highlights: The Reflect and NetPhorest web resources

Networks of proteins and diseases

Gene association networks - Large-scale integration of data and text

Large-scale integration of data and text

Protein association networks: Large-scale integration of data and text

Viewers also liked

Photograph CV Nouman MalikNouman Malik

Memorias II Jornadas de Planificación y Gestión Ambiental

UNELLEZ

Marketing mix

Soumyajit Paikaray

Séminaire du NET

Yann Fontannaz

Mother's daySibabrata Balabantaray

Vinyl Plus Plugs,Dip Moulded Pvc Insulators

Ai Shree Khodiar Plastic

Sitting postureSibabrata Balabantaray

De thi hsg anh 6phuongpham2003

De thi hsg tieng anh 6phuongpham2003

MM_Mentorship_2-28Megan Maier

Nisha parwani B.Sc. Interior Design ( Residential Design Portfolio)

dezyneecole

Axion Suit Magazine Article April 2015Antonios Kypreos

Viewers also liked (12)

Photograph CV Nouman Malik

Memorias II Jornadas de Planificación y Gestión Ambiental

Marketing mix

Séminaire du NET

Mother's day

Vinyl Plus Plugs,Dip Moulded Pvc Insulators

Sitting posture

De thi hsg anh 6

De thi hsg tieng anh 6

MM_Mentorship_2-28

Nisha parwani B.Sc. Interior Design ( Residential Design Portfolio)

Axion Suit Magazine Article April 2015

Similar to The pragmatic text miner: It’s just another type of poorly standardized data

Pragmatic text mining: From literature to electronic health recordsLars Juhl Jensen

Systems biology - Bioinformatics on complete biological systemsLars Juhl Jensen

Pragmatic text mining: From literature to electronic health records

Lars Juhl Jensen

Cellular network biology: Proteome-wide analysis of heterogeneous data

Lars Juhl Jensen

STRING & related databases: Large-scale integration of heterogeneous data

Lars Juhl Jensen

The pragmatic text miner: From literature to electronic health recordsLars Juhl Jensen

One tagger, many uses: Simple text-mining strategies for biomedicine

Lars Juhl Jensen

One tagger, many uses: Illustrating the power of dictionary-based named entit...

Lars Juhl Jensen

Turning literature into databasesLars Juhl Jensen

Networks of proteins and diseasesLars Juhl Jensen

Biomedical literature mining

Lars Juhl Jensen

STRING: Protein association networks

Lars Juhl Jensen

STRING: protein association networks

Lars Juhl Jensen

Network biology - Large-scale integration of data and text

Lars Juhl Jensen

Systems biology: Bioinformatics on complete biological systemLars Juhl Jensen

Network biology: Large-scale data integration and text miningLars Juhl Jensen

Network biology: Large-scale integration of data and text

Lars Juhl Jensen

Advanced bioinformaticsof proteomics datasets

Lars Juhl Jensen

Network biology: Large-scale integration of data and text

Lars Juhl Jensen

Network Biology: Large-scale integration of data and text

Lars Juhl Jensen

Similar to The pragmatic text miner: It’s just another type of poorly standardized data (20)

Pragmatic text mining: From literature to electronic health records

Systems biology - Bioinformatics on complete biological systems

Pragmatic text mining: From literature to electronic health records

Cellular network biology: Proteome-wide analysis of heterogeneous data

STRING & related databases: Large-scale integration of heterogeneous data

The pragmatic text miner: From literature to electronic health records

One tagger, many uses: Simple text-mining strategies for biomedicine

One tagger, many uses: Illustrating the power of dictionary-based named entit...

Turning literature into databases

Networks of proteins and diseases

Biomedical literature mining

STRING: Protein association networks

STRING: protein association networks

Network biology - Large-scale integration of data and text

Systems biology: Bioinformatics on complete biological system

Network biology: Large-scale data integration and text mining

Network biology: Large-scale integration of data and text

Advanced bioinformaticsof proteomics datasets

Network biology: Large-scale integration of data and text

Network Biology: Large-scale integration of data and text

Recently uploaded

Multi-source connectivity as the driver of solar wind variability in the heli...

Sérgio Sacani

The ambient solar wind that flls the heliosphere originates from multiple sources in the solar corona and is highly structured. It is often described as high-speed, relatively homogeneous, plasma streams from coronal holes and slow-speed, highly variable, streams whose source regions are under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify solar wind sources and understand what drives the complexity seen in the heliosphere. By combining magnetic feld modelling and spectroscopic techniques with high-resolution observations and measurements, we show that the solar wind variability detected in situ by Solar Orbiter in March 2022 is driven by spatio-temporal changes in the magnetic connectivity to multiple sources in the solar atmosphere. The magnetic feld footpoints connected to the spacecraft moved from the boundaries of a coronal hole to one active region (12961) and then across to another region (12957). This is refected in the in situ measurements, which show the transition from fast to highly Alfvénic then to slow solar wind that is disrupted by the arrival of a coronal mass ejection. Our results describe solar wind variability at 0.5 au but are applicable to near-Earth observatories.

Penicillin...........................pptx

Cherry

Richard's aventures in two entangled wonderlands

Richard Gill

Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.

justice-and-fairness-ethics with example

azzyixes

Hemoglobin metabolism_pathophysiology.pptx

muralinath2

Lateral Ventricles.pdf very easy good diagrams comprehensive

silvermistyshot

Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...

Sérgio Sacani

Since volcanic activity was first discovered on Io from Voyager images in 1979, changes on Io’s surface have been monitored from both spacecraft and ground-based telescopes. Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images show that a plume deposit from a powerful eruption at Pillan Patera has covered part of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive optics at visible wavelengths.

THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.

Sérgio Sacani

The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.

(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...

Scintica Instrumentation

Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes. In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.

platelets- lifespan -Clot retraction-disorders.pptx

muralinath2

Large scale production of streptomycin.pptx

Cherry

Viksit bharat till 2047 India@2047.pptx

rakeshsharma20142015

filosofia boliviana introducción jsjdjd.pptx

IvanMallco1

Structures and textures of metamorphic rocks

kumarmathi863

SCHIZOPHRENIA Disorder/ Brain Disorder.pdf

SELF-EXPLANATORY

ESR_factors_affect-clinic significance-Pathysiology.pptx

muralinath2

insect taxonomy importance systematics and classification

anitaento25

Circulatory system_ Laplace law. Ohms law.reynaults law,baro-chemo-receptors-...

muralinath2

RNA INTERFERENCE: UNRAVELING GENETIC SILENCING

AADYARAJPANDEY1

Introduction: RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression. It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences. dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants. This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes. What are small ncRNAs? micro RNA (miRNA) short interfering RNA (siRNA) Properties of small non-coding RNA: Involved in silencing mRNA transcripts. Called “small” because they are usually only about 21-24 nucleotides long. Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered). Silence an mRNA by base pairing with some sequence on the mRNA. Discovery of siRNA? The first small RNA: In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the development of the worm C. elegans. Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14. Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions. Types of RNAi ( non coding RNA) MiRNA Length (23-25 nt) Trans acting Binds with target MRNA in mismatch Translation inhibition Si RNA Length 21 nt. Cis acting Bind with target Mrna in perfect complementary sequence Piwi-RNA Length ; 25 to 36 nt. Expressed in Germ Cells Regulates trnasposomes activity MECHANISM OF RNAI: First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces. Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands. The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it. THE RISC COMPLEX: RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA Unwinding of double stranded Si RNA by ATP independent Helicase Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA. DICER: endonuclease (RNase Family III) Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC) One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute ARGONAUTE PROTEIN : 1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA 2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity. MiRNA: The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .

general properties of oerganologametal.ppt

IqrimaNabilatulhusni

Recently uploaded (20)

Multi-source connectivity as the driver of solar wind variability in the heli...

Penicillin...........................pptx

Richard's aventures in two entangled wonderlands

justice-and-fairness-ethics with example

Hemoglobin metabolism_pathophysiology.pptx

Lateral Ventricles.pdf very easy good diagrams comprehensive

Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...

THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.

(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...

platelets- lifespan -Clot retraction-disorders.pptx

Large scale production of streptomycin.pptx

Viksit bharat till 2047 India@2047.pptx

filosofia boliviana introducción jsjdjd.pptx

Structures and textures of metamorphic rocks

SCHIZOPHRENIA Disorder/ Brain Disorder.pdf

ESR_factors_affect-clinic significance-Pathysiology.pptx

insect taxonomy importance systematics and classification

Circulatory system_ Laplace law. Ohms law.reynaults law,baro-chemo-receptors-...

RNA INTERFERENCE: UNRAVELING GENETIC SILENCING

general properties of oerganologametal.ppt