Effects of domain knowledge on reference search with the PubMed database: An experimental study

Open Innovation and Regulatory Challenges in New Modality Development: The Pivotal Role of Contract Development and Manufacturing Organisations in Advancing Antibody Drugs

BACKGROUND

Ensuring regulatory-compliant manufacturing capability is an essential challenge for new treatment modalities, but its internalisation is not easy for pharmaceutical companies, especially start-ups. This study examines the functions and requirements of contracted development and manufacturing organisations (CDMOs) using the development process of antibody medicines as a case study.

METHODS

Utilizing PubMed, Cortellis and Patent Integration databases, this study delves into publication and contractual trends in monoclonal antibody drugs (mAbs) development, alongside an analysis of patent filings by CDMOs, offering a comprehensive overview of the evolving landscape in mAbs innovation.

RESULTS

In the early stages of mAbs development, dedicated bio firms (DBFs) led R&D with superior drug discovery technology but lacked manufacturing capability, which was complemented by CDMOs. This collaboration was an opportunity for CDMOs to expand their capabilities beyond manufacturing technology into antibody drug candidate discovery and structural optimisation technology. From mid-development onwards, it established a technology platform based on these capabilities and developed and established partnerships with existing pharmaceutical companies, including mega pharma.

CONCLUSIONS

The impact of institutions and regulations on the innovation process was assessed during this development process. These findings are expected to provide valuable insights into the innovation system for new modalities.

Analysis of PubMed User Sessions Using a Full-Day PubMed Query Log: A Comparison of Experienced and Nonexperienced PubMed Users

Background

PubMed is the largest biomedical bibliographic information source on the Internet. PubMed has been considered one of the most important and reliable sources of up-to-date health care evidence. Previous studies examined the effects of domain expertise/knowledge on search performance using PubMed. However, very little is known about PubMed users’ knowledge of information retrieval (IR) functions and their usage in query formulation.

Objective

The purpose of this study was to shed light on how experienced/nonexperienced PubMed users perform their search queries by analyzing a full-day query log. Our hypotheses were that (1) experienced PubMed users who use system functions quickly retrieve relevant documents and (2) nonexperienced PubMed users who do not use them have longer search sessions than experienced users.

Methods

To test these hypotheses, we analyzed PubMed query log data containing nearly 3 million queries. User sessions were divided into two categories: experienced and nonexperienced. We compared experienced and nonexperienced users per number of sessions, and experienced and nonexperienced user sessions per session length, with a focus on how fast they completed their sessions.

Results

To test our hypotheses, we measured how successful information retrieval was (at retrieving relevant documents), represented as the decrease rates of experienced and nonexperienced users from a session length of 1 to 2, 3, 4, and 5. The decrease rate (from a session length of 1 to 2) of the experienced users was significantly larger than that of the nonexperienced groups.

Conclusions

Experienced PubMed users retrieve relevant documents more quickly than nonexperienced PubMed users in terms of session length.

Domain knowledge and data quality perceptions in genome curation work

Purpose

– The purpose of this paper is to understand genomics scientists’ perceptions in data quality assurances based on their domain knowledge.

Design/methodology/approach

– The study used a survey method to collect responses from 149 genomics scientists grouped by domain knowledge. They ranked the top-five quality criteria based on hypothetical curation scenarios. The results were compared using χ2 test.

Findings

– Scientists with domain knowledge of biology, bioinformatics, and computational science did not reach a consensus in ranking data quality criteria. Findings showed that biologists cared more about curated data that can be concise and traceable. They were also concerned about skills dealing with information overloading. Computational scientists on the other hand value making curation understandable. They paid more attention to the specific skills for data wrangling.

Originality/value

– This study takes a new approach in comparing the data quality perceptions for scientists across different domains of knowledge. Few studies have been able to synthesize models to interpret data quality perception across domains. The findings may help develop data quality assurance policies, training seminars, and maximize the efficiency of genome data management.

A study of the influence of task familiarity on user behaviors and performance with a MeSH term suggestion interface for PubMed bibliographic search

PURPOSE

Previous research has shown that information seekers in biomedical domain need more support in formulating their queries. A user study was conducted to evaluate the effectiveness of a metadata based query suggestion interface for PubMed bibliographic search. The study also investigated the impact of search task familiarity on search behaviors and the effectiveness of the interface.

METHODS

A real user, user search request and real system approach was used for the study. Unlike tradition IR evaluation, where assigned tasks were used, the participants were asked to search requests of their own. Forty-four researchers in Health Sciences participated in the evaluation - each conducted two research requests of their own, alternately with the proposed interface and the PubMed baseline. Several performance criteria were measured to assess the potential benefits of the experimental interface, including users' assessment of their original and eventual queries, the perceived usefulness of the interfaces, satisfaction with the search results, and the average relevance score of the saved records.

RESULTS

The results show that, when searching for an unfamiliar topic, users were more likely to change their queries, indicating the effect of familiarity on search behaviors. The results also show that the interface scored higher on several of the performance criteria, such as the "goodness" of the queries, perceived usefulness, and user satisfaction. Furthermore, in line with our hypothesis, the proposed interface was relatively more effective when less familiar search requests were attempted.

CONCLUSIONS

Results indicate that there is a selective compatibility between search familiarity and search interface. One implication of the research for system evaluation is the importance of taking into consideration task familiarity when assessing the effectiveness of interactive IR systems.

Supporting effective health and biomedical information retrieval and navigation: a novel facet view interface evaluation

There is a need to provide a more effective user interface to facilitate non-domain experts' health information seeking in authoritative online databases such as MEDLINE. We developed a new topic cluster based information navigation system called SimMed. Instead of offering a list of documents, SimMed presents users with a list of ranked clusters. Topically similar documents are grouped together to provide users with a better overview of the search results and to support exploration of similar literature within a cluster. We conducted an empirical user study to compare SimMed to a traditional document list based search interface. A total of 42 study participants were recruited to use both interfaces for health information exploration search tasks. The results showed that SimMed is more effective in terms of users' perceived topic knowledge changes and their engagement in user-system interactions. We also developed a new metric to assess users' efforts to find relevant citations. On average, users need significantly fewer clicks to find relevant information in SimMed than in the baseline system. Comments from study participants indicated that SimMed is more helpful in finding similar citations, providing related medical terms, and presenting better organized search results, particularly when the initial search is unsatisfactory. Findings from the study shed light on future health and biomedical information retrieval system and interface designs.