The dynamics and social organization of innovation in the field of oncology/Bibliography

Papers and resources

General

Use of absrtacts

• Assessing the Eventual Publication of Clinical Trial Abstracts Submitted to a Large Annual Oncology Meeting

Document tagging and other text-mining

• OpenMinTeD, European text-mining infrastructure
• NCBI text mining web services
• EuropePMC text mined annotations

Funding data

• Funding Data from Publication Acknowledgements: Coverage, Uses and Limitations

Innovation dynamics

• A triple helix model of medical innovation: Supply, demand, and technological capabilities in terms of Medical Subject Headings

Topical burst detection

• Bursty and Hierarchical Structure in Streams, implementations in C, python
• Mapping topics and topic bursts in PNAS

Name disambiguation

• Author name disambiguation, a recent review
• Exploiting citation networks for large-scale author name disambiguation, a recent paper from ppl at ETH-Zurich

Ontologies

• Disease Ontology

Evolving communities

• Evolving network structure of academic institutions

Word embedding

Algorithm and improvements

• king - man + woman is queen; but why?
• What are some interesting Word2Vec results?
• Linguistic Regularities in Sparse and Explicit Word Representations
• Document Classification by Inversion of Distributed Language Representations
• A Dual Embedding Space Model for Document Ranking

Changes in meaning

• Diachronic Word Embeddings Reveal Statistical Laws of Semantic Change
• Statistically Significant Detection of Linguistic Change

Stochastic block models and description length minimization

• Inferring the mesoscale structure of layered, edge-valued and time-varying networks
• Hierarchical Block Structures and High-Resolution Model Selection in Large Networks
• Model Selection and Hypothesis Testing for Large-Scale Network Models with Overlapping Groups

Visualizations

• Visualizing genomic testing in the cancer clinical trials portfolio

Medical ontologies

• The NCI has a dictionary of cancer terms with 8,389 terms

• The NCI has a drug dictionary

• the NCI has a dictionary of genetics terms

• See also the NCI list of cancer types

There are also more sophisticated ontologies:

• For instance, there is an NCI Thesaurus
• BioPortal keeps a database of ontologies

News

Social media buzz

• Social (Media) Oncology Project

Core set hypothesis

• A Countdown: Top 10 Problems With NCI-Designated Cancer Centers, item 2.

Transparency

Sanofi, Novartis, NCI, Ranbaxy top missing data list as Shire most transparent

ASCO and ESMO

ESMO's not what it used to be—and that's a good thing, executives say

Research Seminars

Gabriel Varela

• BRCA Patients and Clinical Collectives: New Configurations of Action in Cancer Genetics Practices Pascale Bourret