Evidence map›Paper›PMID 25618216›Full record

ArticleComputers in biology and medicine2015

Representing and extracting lung cancer study metadata: study objective and study design.

Jean I Garcia-Gathright, Andrea Oh, Phillip A Abarca, Mary Han, William Sago, Marshall L Spiegel, Brian Wolf, Edward B Garon, Alex A T Bui, Denise R Aberle

Open access · greenAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Computers in biology and medicine, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
0.3field-weighted citation impact, top 38% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed, 3 citations in OpenAlex.

  1. Article
  2. Toward patient-tailored summarization of lung cancer literature.... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics · 2016
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors at 1 institution in 1 country.

Jean I Garcia-GathrightDepartment of Bioengineering, University of California, 924 Westwood Boulevard, Suite 420, Los Angeles, CA 90024, USA. Electronic address: jigarcia@ucla.edu.
Andrea OhDepartment of Radiological Sciences, University of California, 924 Westwood Boulevard, Suite 420, Los Angeles, CA 90024, USA.
Phillip A AbarcaDepartment of Medicine - Division of Hematology-Oncology, University of California, 924 Westwood Boulevard, Suite 200, Los Angeles, CA 90024, USA.
Mary HanDepartment of Medicine - Division of Hematology-Oncology, University of California, 924 Westwood Boulevard, Suite 200, Los Angeles, CA 90024, USA.
William SagoDepartment of Medicine - Division of Hematology-Oncology, University of California, 924 Westwood Boulevard, Suite 200, Los Angeles, CA 90024, USA.
Marshall L SpiegelDepartment of Medicine - Division of Hematology-Oncology, University of California, 924 Westwood Boulevard, Suite 200, Los Angeles, CA 90024, USA.
Brian WolfDepartment of Medicine - Division of Hematology-Oncology, University of California, 924 Westwood Boulevard, Suite 200, Los Angeles, CA 90024, USA.
Edward B GaronDepartment of Medicine - Division of Hematology-Oncology, University of California, 924 Westwood Boulevard, Suite 200, Los Angeles, CA 90024, USA.
Alex A T BuiDepartment of Bioengineering, University of California, 924 Westwood Boulevard, Suite 420, Los Angeles, CA 90024, USA; Department of Radiological Sciences, University of California, 924 Westwood Boulevard, Suite 420, Los Angeles, CA 90024, USA.
Denise R AberleDepartment of Bioengineering, University of California, 924 Westwood Boulevard, Suite 420, Los Angeles, CA 90024, USA; Department of Radiological Sciences, University of California, 924 Westwood Boulevard, Suite 420, Los Angeles, CA 90024, USA.
University of California, Los Angeles · US

Funding

Training Program for Imaging Based Medical InformaticsT15LM007356 · NLM · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI BUI, ALEX · 2002 to 2011
$5.0M
Data Structuring and Visualization System for Neuro-oncologyR01LM009961 · NLM · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI TAIRA, RICKY K. · 2009 to 2010
$1.7M
RUMI: A patient portal for retrieving understandable medical informationR01LM011333 · NLM · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI BUI, ALEX · 2012 to 2015
$1.3M
Inhibiting EGFR and ER pathways in NSCLCK23CA149079 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI GARON, EDWARD B · 2011 to 2015
$826k
NCI NIH HHS K23 CA149079NCI NIH HHS K23CA149079NLM NIH HHS R01 LM009961NLM NIH HHS R01-LM009961NLM NIH HHS R01 LM011333NLM NIH HHS T15 LM007356NLM NIH HHS T15-LM007356
6 · The paper itself

Abstract

This paper describes the information retrieval step in Casama (Contextualized Semantic Maps), a project that summarizes and contextualizes current research papers on driver mutations in non-small cell lung cancer. Casama׳s representation of lung cancer studies aims to capture elements that will assist an end-user in retrieving studies and, importantly, judging their strength. This paper focuses on two types of study metadata: study objective and study design. 430 abstracts on EGFR and ALK mutations in lung cancer were annotated manually. Casama׳s support vector machine (SVM) automatically classified the abstracts by study objective with as much as 129% higher F-scores compared to PubMed׳s built-in filters. A second SVM classified the abstracts by epidemiological study design, suggesting strength of evidence at a more granular level than in previous work. The classification results and the top features determined by the classifiers suggest that this scheme would be generalizable to other mutations in lung cancer, as well as studies on driver mutations in other cancer domains.

Indexed as

Databases, FactualLung NeoplasmsResearch DesignComputational BiologyHumansInformation Storage and RetrievalMutationPrognosisROC CurveSupport Vector MachineAutomatic summarizationInformation retrievalQuality of evidence

Identifiers

PMID25618216
PMCPMC4331232
OpenAlexW2169254978

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.