Engineering topics

de Waard, Anita

Publications and source records attributed to de Waard, Anita.

3 records

DOE OSTI2022

A roadmap for the functional annotation of protein families: a community perspective

Over the last 25 years, biology has entered the genomic era and is becoming a science of ‘big data’. Most interpretations of genomic analyses rely on accurate functional annotations of the proteins encoded by more than 500 000 genomes sequenced to date. By different estimates, only half the predicted sequenced proteins carry an accurate functional annotation, and this percentage varies drastically between different organismal lineages. Such a large gap in knowledge hampers all aspects of biological enterprise and, thereby, is standing in the way of genomic biology reaching its full potential. A brainstorming meeting to address this issue funded by the National Science Foundation was held during 3–4 February 2022. Bringing together data scientists, biocurators, computational biologists and experimentalists within the same venue allowed for a comprehensive assessment of the current state of functional annotations of protein families. Further, major issues that were obstructing the field were identified and discussed, which ultimately allowed for the proposal of solutions on how to move forward.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Overview of the Second Workshop on Scholarly Document Processing

With the ever-increasing pace of research and high volume of scholarly communication, scholars face a daunting task. Not only must they keep up with the growing literature in their own and related fields, scholars increasingly also need to rebut pseudo-science and disinformation. These needs have motivated an increasing focus on computational methods for enhancing search, summarization, and analysis of scholarly documents. However, the various strands of research on scholarly document processing remain fragmented. To reach out to the broader NLP and AI/ML community, pool distributed efforts in this area, and enable shared access to published research, we held the 2nd Workshop on Scholarly Document Processing (SDP) at NAACL 2021 as a virtual event (https://sdproc.org/2021/). The SDP workshop consisted of a research track, three invited talks, and three Shared Tasks (LongSumm 2021, SCIVER, and 3C). The program was geared towards the application of NLP, information retrieval, and data mining for scholarly documents, with an emphasis on identifying and providing solutions to open challenges.

Beltagy, Iz↗