About

Developed as part of the BioText project at the University of California, Berkeley, the BioText Search Engine is a freely available Web-based application that provides biologists with new ways to access the scientific literature.

The interface has been carefully designed according to usability principles and techniques. The system uses Lucene for the underlying indexing, and users can use all the Lucene operators in their search queries.

The search engine is a work in progress and more functionality is being added over time.



NEWS



  • October 2007: Update! Table search, a larger collection, and improved highlighting!

The BioText Search Engine now allows users to search in tables. When the "table" view is selected, BioText searches in article titles, table captions, and table contents.





  • August 2007: Update! Improved indexing, full-text excerpts and bigger collection!

The old "Abstract (List View)" has changed to "Full Text & Abstract" view. This view searches the full text of articles (in addition to title, author, and abstract information) and returns full-text excerpts that match users' queries. Three selection boxes at the top ("ABSTRACTS", "FULL-TEXT EXCERPTS" and "FIGURES" allow users to choose what the view displays.





  • July 2007: Poster presented at ECCB/ISMB in Vienna

Hearst, M.A., Wooldridge, M.A., Ye, J. and Divoli, A. (2007) "Showing Figures and Captions in the Biotext Journal Search Engine", ISMB/ECCB 2007, Vienna, Austria (PDF)



  • June 2007: Paper presented at the BioNLP Workshop at ACL in Prague

Hearst, M.A., Divoli, A., Wooldridge, M.A. and Ye, J. (2007) "Exploring the Efficacy of Caption Search for Bioscience Journal Search Interfaces", BioNLP Workshop at ACL 2007, Prague, Czech Republic (PDF)



  • June 2007: Paper published in Bioinformatics advanced access

Hearst, M.A., Divoli, A., Guturu, H., Ksikes, A., Nakov, P., Wooldridge, M.A. and Ye, J. (2007) "BioText Search Engine: beyond abstract search", Bioinformatics, 23: 2196-2197 (PDF)



  • May 2007: The BioText Search Engine has been launched

Three views allow different types of browsing:


Search over abstracts.
See each article's figures.

Abstracts (List View): Allows users to search over titles, abstracts and authors. Returns a list of abstracts showing the figures associated with each article.


Search over captions.
See matching figures in a list.
Captions (List View): Allows users to search over captions. Returns a list of captions and their figures.



Search over captions.
See matching figures in a grid.
Captions (Grid View): Allows users to search over captions. Returns figures and truncated captions in a grid arrangement.



The Collection

The system indexes all open access articles available at PubMed Central. New articles are indexed daily. The current collection consists of more than 300 journals, 40,000 articles, 100,000 figures, and 60,000 tables.


Journals indexed:

AIDS Research and Therapy
AIDS and Behavior
Acta Neuropathologica
Acta Veterinaria Scandinavica
Algorithms for Molecular Biology
American Journal of Community Psychology
Amphibian and Reptile Conservation
Analytical and Bioanalytical Chemistry
Annals of Biomedical Engineering
Annals of Clinical Microbiology and Antimicrobials
Annals of General Hospital Psychiatry
Annals of General Psychiatry
Annals of Hematology
Annals of Surgical Innovation and Research
Annals of Surgical Oncology
Apoptosis
Applied Microbiology and Biotechnology
Applied Psychophysiology and Biofeedback
Archives for Dermatological Research
Archives of Dermatological Research
Archives of Environmental Contamination and Toxicology
Archives of Gynecology and Obstetrics
Archives of Orthopaedic and Trauma Surgery
Archives of Sexual Behavior
Archives of Toxicology
Arthritis Research & Therapy
Arthritis Research
Australia and New Zealand Health Policy
BMC Anesthesiology
BMC Biochemistry
BMC Bioinformatics
BMC Biology
BMC Biotechnology
BMC Blood Disorders
BMC Cancer
BMC Cardiovascular Disorders
BMC Cell Biology
BMC Chemical Biology
BMC Clinical Pathology
BMC Clinical Pharmacology
BMC Complementary and Alternative Medicine
BMC Dermatology
BMC Developmental Biology
BMC Ear, Nose and Throat Disorders
BMC Ear, Nose, and Throat Disorders
BMC Ecology
BMC Emergency Medicine
BMC Endocrine Disorders
BMC Evolutionary Biology
BMC Family Practice
BMC Gastroenterology
BMC Genetics
BMC Genomics
BMC Geriatrics
BMC Health Services Research
BMC Immunology
BMC Infectious Diseases
BMC International Health and Human Rights
BMC Medical Education
BMC Medical Ethics
BMC Medical Genetics
BMC Medical Imaging
BMC Medical Informatics and Decision Making
BMC Medical Research Methodology
BMC Medicine
BMC Microbiology
BMC Molecular Biology
BMC Musculoskeletal Disorders
BMC Nephrology
BMC Neurology
BMC Neuroscience
BMC Nuclear Medicine
BMC Nursing
BMC Ophthalmology
BMC Oral Health
BMC Palliative Care
BMC Pediatrics
BMC Pharmacology
BMC Physiology
BMC Plant Biology
BMC Pregnancy and Childbirth
BMC Psychiatry
BMC Public Health
BMC Pulmonary Medicine
BMC Structural Biology
BMC Surgery
BMC Systems Biology
BMC Urology
BMC Veterinary Research
BMC Women's Health
Behavior Genetics
Behavioral and Brain Functions
Beilstein Journal of Organic Chemistry
BioMedical Engineering OnLine
Biological Procedures Online
Biology Direct
Biomagnetic Research and Technology
Biomechanics and Modeling in Mechanobiology
Biomedical Digital Libraries
Bioprocess and Biosystems Engineering
Biopsychosocial Medicine
Biotechnology Letters
Breast Cancer Research and Treatment
Breast Cancer Research
British Journal of Clinical Pharmacology
Calcified Tissue International
Cancer Causes & Control
Cancer Cell International
Cancer Immunology, Immunotherapy
Carbon Balance and Management
Cardiovascular Diabetology
Cardiovascular Drugs and Therapy
Cardiovascular Ultrasound
Cardiovascular and Interventional Radiology
Cell Communication and Signaling
Cell Division
Cell and Chromosome
Cerebrospinal Fluid Research
Chemistry Central Journal
Child and Adolescent Psychiatry and Mental Health
Child's Nervous System
Chinese Medicine
Chiropractic & Osteopathy
Chromosoma
Clinical Autonomic Research
Clinical Practice and Epidemiology in Mental Health
Clinical Rheumatology
Clinical and Experimental Immunology
Clinical and Molecular Allergy
Clinical practice and epidemiology in mental health
Community Mental Health Journal
Comparative Hepatology
Conflict and Health
Cost Effectiveness and Resource Allocation
Cough
Critical Care
Culture, Medicine and Psychiatry
Current Controlled Trials in Cardiovascular Medicine
CytoJournal
Diabetologia
Diagnostic Pathology
Digestive Diseases and Sciences
Diseases of the Colon and Rectum
Documenta Ophthalmologica. Advances in Ophthalmology
Dynamic Medicine
Dysphagia
eHealth International
Emergency Radiology
Emerging Themes in Epidemiology
Environmental Health Perspectives
Environmental Health: A Global Access Science Source
Environmental Health
Environmental Management
Environmental health perspectives.
Epidemiologic Perspectives & Innovations
European Archives of Oto-Rhino-Laryngology
European Archives of Psychiatry and Clinical Neuroscience
European Biophysics Journal
European Child & Adolescent Psychiatry
European Journal of Applied Physiology
European Journal of Clinical Microbiology & Infectious Diseases
European Journal of Clinical Pharmacology
European Journal of Epidemiology
European Journal of Health Economics
European Journal of Nuclear Medicine and Molecular Imaging
European Journal of Nutrition
European Journal of Pediatrics
European Radiology
European Spine Journal
Evidence-based Complementary and Alternative Medicine
Experimental Brain Research
Familial Cancer
Filaria Journal
Frontiers in Zoology
Genetic Vaccines and Therapy
Genome Biology
Geochemical Transactions
Globalization and Health
Harm Reduction Journal
Head & Face Medicine
Health Research Policy and Systems
Health Services Research
Health and Quality of Life Outcomes
Human Genetics
Human Resources for Health
Immunity & Ageing
Immunogenetics
Immunology
Immunome Research
Implementation Science
Indian Pacing and Electrophysiology Journal
Infectious Agents and Cancer
Infectious Diseases in Obstetrics and Gynecology
Intensive Care Medicine
International Archives of Occupational and Environmental Health
International Breastfeeding Journal
International Journal for Equity in Health
International Journal of Behavioral Nutrition and Physical Activity
International Journal of Biological Sciences
International Journal of Health Geographics
International Journal of Medical Sciences
International Seminars in Surgical Oncology
Investigational New Drugs
Journal of Abnormal Child Psychology
Journal of Autoimmune Diseases
Journal of Biological Inorganic Chemistry
Journal of Biology
Journal of Biomedical Discovery and Collaboration
Journal of Biomedicine and Biotechnology
Journal of Biomolecular Nmr
Journal of Brachial Plexus and Peripheral Nerve Injury
Journal of Burns and Wounds
Journal of Carcinogenesis
Journal of Cardiothoracic Surgery
Journal of Chemical Ecology
Journal of Circadian Rhythms
Journal of Clinical Immunology
Journal of Digital Imaging
Journal of Ethnobiology and Ethnomedicine
Journal of Experimental & Clinical Assisted Reproduction
Journal of Fluorescence
Journal of Gastrointestinal Surgery
Journal of General Internal Medicine
Journal of Human Genetics
Journal of Immune Based Therapies and Vaccines
Journal of Inflammation
Journal of Insect Science
Journal of Materials Science. Materials in Medicine
Journal of Medical Case Reports
Journal of Membrane Biology
Journal of Molecular Evolution
Journal of Molecular Signaling
Journal of Nanobiotechnology
Journal of Negative Results in Biomedicine
Journal of Neuro-Oncology
Journal of NeuroEngineering and Rehabilitation
Journal of Neuroinflammation
Journal of Neurology
Journal of Occupational Medicine and Toxicology
Journal of Occupational Rehabilitation
Journal of Orthopaedic Surgery and Research
Journal of Physiology
Journal of Structural and Functional Genomics
Journal of Translational Medicine
Journal of Urban Health
Journal of the Association for Research in Otolaryngology
Kinetoplastid Biology and Disease
Knee Surgery, Sports Traumatology, Arthroscopy
Lipids in Health and Disease
Malaria Journal
Mammalian Genome
Marine Biotechnology
Maternal and Child Health Journal
Mediators of Inflammation
Medical & Biological Engineering & Computing
Medical History
Medical Immunology
Microbial Cell Factories
Microbial Ecology
Molecular Cancer
Molecular Genetics and Genomics
Molecular Imaging and Biology
Molecular Neurodegeneration
Molecular Pain
Molecular Systems Biology
Molecular and Cellular Biochemistry
Neural Development
Neurochemical Research
Neurogenetics
Neuroradiology
Neurosurgical Review
Nonlinear Biomedical Physics
Nuclear Receptor
Nucleic Acids Research
Nucleic Acids ResearchNucleic Acids Research
Nutrition & Metabolism
Nutrition Journal
Oecologia
Orphanet Journal of Rare Diseases
Osteopathic Medicine and Primary Care
Osteoporosis International
PLoS Biology
PLoS Clinical Trials
PLoS Computational Biology
PLoS Genetics
PLoS Medicine
PLoS ONE
PLoS Pathogens
PPAR Research
Particle and Fibre Toxicology
Pediatric Nephrology (Berlin, Germany)
Pediatric Radiology
Pediatric Rheumatology Online Journal
Pflugers Archiv
Pharmaceutical Research
Pharmacy World & Science
Philosophical Transactions of the Royal Society B: Biological Sciences
Philosophy, Ethics, and Humanities in Medicine
Pituitary
Plant Methods
Plant Molecular Biology
Population Health Metrics
Preventing Chronic Disease
Proceedings of the Royal Society B: Biological Sciences
Proteome Science
Psychopharmacologia
Quality of Life Research
Radiation Oncology (London, England)
Reproductive Biology and Endocrinology
Reproductive Health
Respiratory Research
Retrovirology
Reviews in Endocrine & Metabolic Disorders
Saline Systems
Sarcoma
Scoliosis
Sexual Abuse
Skeletal Radiology
Source Code for Biology and Medicine
Substance Abuse Treatment, Prevention, and Policy
Surgical and Radiologic Anatomy
TAG: Theoretical and Applied Genetics
Theoretical Biology & Medical Modelling
Theoretical Biology and Medical Modelling
Thrombosis Journal
Trials
The Ulster Medical Journal
Virchows Archiv
Virology Journal
World Journal of Emergency Surgery
World Journal of Surgery
World Journal of Surgical Oncology
World Journal of Urology

References

BioText Search Engine: beyond abstract search
Marti A. Hearst, Anna Divoli, Harendra Guturu, Alex Ksikes, Preslav Nakov, Michael A. Wooldridge and Jerry Ye
Bioinformatics 2007; doi: 10.1093/bioinformatics/btm301 (PDF)

Exploring the efficacy of caption search for bioscience journal search interfaces
Marti A. Hearst, Anna Divoli, Jerry Ye and Michael A. Wooldridge
Paper at ACL 2007 Workshop on BioNLP, Prague, Czech Republic (PDF)

Showing Figures and Captions in the Biotext Journal Search Engine
Marti A. Hearst, Michael A. Wooldridge, Jerry Ye and Anna Divoli
PLoS Poster at ISMB/ECCB 2007, Vienna, Austria (PDF)