International Society For Computational Biology Research Articles

Progress with Repository-based Annotation Infrastructure for Biodiversity Applications

Rapid development since the 1980s of technologies for analysing texts, has led not only to widespread employment of text 'mining', but also to now-pervasive large language model artificial intelligence (AI) applications. However, building new, concise, data resources from historic, as well as contemporary scientific literature, which can be employed efficiently at scale by automation and which have long-term value for the research community, has proved more elusive. Efforts at codifying analyses, such as the Text Encoding Initiative (TEI), date from the early 1990s and were initially driven by the social sciences and humanities (SSH) and linguistics communities, and extended with multiple XML-based tagging schemes, including in biodiversity (Miller et al. 2012). In 2010, the Bio-Ontologies Special Interest Group (of the International Society for Computational Biology) presented its Annotation Ontology (AO), incorporating JavaScript Object Notation and broadening previous XML-based approaches (Ciccarese et al. 2011). From 2011, the Open Annotation Data Model (OADM) (Sanderson et al. 2013) focused on cross-domain standards with utility for Web 3.0, leading to the W3C Web Annotation Data Model (WADM) Recommendation in February 2017*1 and the potential for unifying the multiplicity of already-in-use tagging approaches. This continual evolution has made the preservation of investment using annotation methods, and in particular of the connections between annotations and their context in source literature, particularly challenging. Infrastructure that entered service during the intervening years does not yet support WADM, and has only recently started to address the parallel emergence of page imagery-based standards such as the International Image Interoperability Framework (IIIF). Notably, IIIF instruments such as Mirador-2, which has been employed widely for manual creation and editing of annotations in SSH, continue to employ the now-deprecated OADM. Although multiple efforts now address combining IIIF and TEI text coordinate systems, they are currently fundamentally incompatible. However, emerging repository technologies enable preservation of annotation investment to be accomplished comprehensively for the first time. Native IIIF support enables interactive previewing of annotations within repository graphical user interfaces and dynamic serialisation technologies provide compatibility with existing XML-based infrastructures. Repository access controls can permit experts to trace annotation sources in original texts even if the literature is not publicly accessible, e.g., due to copyright restriction. This is of paramount importance, not only because surrounding context can be crucial to qualify formal terms that have been annotated, such as collecting country. Also, contemporary automated text mining—essential for operation at the scale of known biodiversity literature—is not 100% accurate and manual checking of uncertainties is currently essential. On-going improvement of language analysis tools through AI integration offers significant future gains from reprocessing literature and updating annotation data resources. Nevertheless, without effective preservation of digitized literature, as well as annotations, this enrichment will not be possible—and today's investments in gathering together, as well as analysing scientific literature will be devalued or lost. We report new functionality included in the InvenioRDM*2 Free and Open Source Software (FOSS) repository software platform, which natively supports IIIF and WADM. InvenioRDM development and maintenance is funded and managed by an international consortium. From late 2023, the InvenioRDM-based ZenodoRDM update*3 will display annotations on biodiversity literature interactively. Significantly, the Biodiversity Literature Repository (BLR) is a Zenodo Community. BLR automatically notifies the Global Biodiversity Information Facility (GBIF) of new taxonomic data and GBIF downloads and integrates this into its service. Moreover, an annotation service based on the WADM-native Mirador-3 FOSS IIIF viewer has now been developed and will enter service with ZenodoRDM. This enables editing of biodiversity annotations from within the repository interface, as well as automated updating of taxonomic information products provided to other major infrastructures such as GBIF. Two aspects of this ZenodoRDM annotation service are presented: dynamic transformation of (preservable) WADM annotations for consumption by contemporary IIIF-compliant applications such as Mirador-3, as well as for Plazi TreatmentBank/GBIF compatibility authentication and task organization permitting management of groups of expert contributors performing annotation enrichment tasks directly through the ZenodoRDM graphical user interface (GUI) dynamic transformation of (preservable) WADM annotations for consumption by contemporary IIIF-compliant applications such as Mirador-3, as well as for Plazi TreatmentBank/GBIF compatibility authentication and task organization permitting management of groups of expert contributors performing annotation enrichment tasks directly through the ZenodoRDM graphical user interface (GUI) Workflows for editing existing biodiversity annotations, as well as origination of new annotations, need to be tailored for specific tasks—e.g., unifying geographic collecting location definitions in historic reports—via configurable dialogs for contributors and controlled vocabularies. Selectively populating workflows with annotations according to a task definition is also important to avoid cluttering the editing GUI with non-essential information. Updated annotations are integrated into a new annotation collection upon completion of a task, before updating repository records. Current work on annotation workflows for SSH applications is also reported. The ZenodoRDM biodiversity annotation service implements a generic repository micro-service API, and the implementation of similar services for other repository software platforms is discussed.

Characterizing domain-specific open educational resources by linking ISCB Communities of Special Interest to Wikipedia.

MotivationWikipedia is one of the most important channels for the public communication of science and is frequently accessed as an educational resource in computational biology. Joint efforts between the International Society for Computational Biology (ISCB) and the Computational Biology taskforce of WikiProject Molecular Biology (a group of expert Wikipedia editors) have considerably improved computational biology representation on Wikipedia in recent years. However, there is still an urgent need for further improvement in quality, especially when compared to related scientific fields such as genetics and medicine. Facilitating involvement of members from ISCB Communities of Special Interest (COSIs) would improve a vital open education resource in computational biology, additionally allowing COSIs to provide a quality educational resource highly specific to their subfield.ResultsWe generate a list of around 1500 English Wikipedia articles relating to computational biology and describe the development of a binary COSI-Article matrix, linking COSIs to relevant articles and thereby defining domain-specific open educational resources. Our analysis of the COSI-Article matrix data provides a quantitative assessment of computational biology representation on Wikipedia against other fields and at a COSI-specific level. Furthermore, we conducted similarity analysis and subsequent clustering of COSI-Article data to provide insight into potential relationships between COSIs. Finally, based on our analysis, we suggest courses of action to improve the quality of computational biology representation on Wikipedia.

Analysis of scientific society honors reveals disparities.

Delivering a keynote talk at a conference organized by a scientific society or being named as a fellow by such a society indicates that a scientist is held in high regard by their colleagues. To explore if the distribution of such indicators of esteem in the field of bioinformatics reflects the composition of this field, we compared the gender, name origin, and country of affiliation of 412 honorees from the "International Society for Computational Biology" (75 fellows and 337 keynote speakers) with over 170,000 last authorships on computational biology papers between 1993 and 2019. The proportion of honors bestowed on women was similar to that of the field's overall last authorship rate. However, names of East Asian origin have been persistently underrepresented among honorees. Moreover, there were roughly twice as many honors bestowed on scientists with an affiliation in the United States as expected based on literature authorship. A record of this paper's transparent peer review process is included in the supplemental information.

ISCB Honors 2021 Award Recipients Peer Bork, Barbara Engelhardt, Ben Raphael, Teresa Attwood.

Annually, the International Society for Computational Biology (ISCB) recognizes three outstanding researchers for significant scientific contributions to the field of bioinformatics and computational biology, as well as one individual for exemplary service to the field. ISCB is honored to announce the 2021 Accomplishments by a Senior Scientist Awardee, Overton Prize recipient, Innovator Awardee and Outstanding Contributions to ISCB Awardee.Peer Bork, EMBL Heidelberg, is the winner of the Accomplishments by a Senior Scientist Award. Barbara Engelhardt, Princeton University, is the Overton Prize winner. Ben Raphael, Princeton University, is the winner of the ISCB Innovator Award. Teresa Attwood, Manchester University, has been selected as the winner of the Outstanding Contributions to ISCB Award.Martin Vingron, Chair, ISCB Awards Committee noted, ‘As chair of the Awards Committee it gives me great pleasure to convey my heart-felt congratulations to this year’s awardees. Our community, as represented by the committee, admires these individuals’ outstanding achievements in research, training, and outreach.’

2019 Outstanding Contributions to ISCB Awarded to Barb Bryant.

2019 Outstanding Contributions to ISCB Awarded to Barb Bryant.

The 2018 Bioinformatics Open Source Conference (GCCBOSC 2018).

In 2018, the annual Bioinformatics Open Source Conference was held for the first time in conjunction with the Galaxy Community Conference, as an experiment to see if we could reach people in the bioinformatics community who aren’t part of the audience attracted by ISMB. Held in June 2018 at Reed College in Portland, Oregon, GCCBOSC (Galaxy Community Conference and Bioinformatics Open Source Conference) attracted over 300 participants from around the world. The meeting started with two days of training, followed by two days of talks and poster/demo sessions (with some joint and some parallel sessions). The joint sessions included well-received keynote talks by Tracy Teal, Fernando Pérez and Lucia Peixoto, as well as a panel discussion about documentation and training. After the main meeting, many attendees stayed for up to four additional collaboration days, an extended version of the Codefests that have been held in conjunction with previous BOSCs. GCCBOSC was a successful experiment. The organizers concluded that the best way to serve the broadest community of potential BOSC attendees will be to partner some years with the International Society for Computational Biology (ISMB) and others with GCC.

Message from the ISCB: 2018 Outstanding Contributions to ISCB Award: Russ Altman.

Message from the ISCB: 2018 Outstanding Contributions to ISCB Award: Russ Altman.

Establishment of “The South African Bioinformatics Student Council” and Activity Highlights

The South African Bioinformatics Student Council (SASBiSC) in bioinformatics has been set up to increase the visibility of bioinformatics as well as to filter information to students within the field regarding job, funding and workshop opportunities as they arise. This is a short description of the process of setting up a national Student Council for Bioinformatics in South Africa, affiliating to the International Society for Computational Biology (ISCB). We also report two examples of activities that were carried out over the last two years that are: 1) participation in the SciFest Africa; and 2) the organisation of the first Bioinformatics Student Symposium.  We hope that our experience and methods for the creation of SASBiSC and of collaborative communities can be useful to others who might want to do the same.

The ISCB Student Council Internship Program: Expanding computational biology capacity worldwide.

Education and training are two essential ingredients for a successful career. On one hand, universities provide students a curriculum for specializing in one’s field of study, and on the other, internships complement coursework and provide invaluable training experience for a fruitful career. Consequently, undergraduates and graduates are encouraged to undertake an internship during the course of their degree. The opportunity to explore one’s research interests in the early stages of their education is important for students because it improves their skill set and gives their career a boost. In the long term, this helps to close the gap between skills and employability among students across the globe and balance the research capacity in the field of computational biology. However, training opportunities are often scarce for computational biology students, particularly for those who reside in less-privileged regions. Aimed at helping students develop research and academic skills in computational biology and alleviating the divide across countries, the Student Council of the International Society for Computational Biology introduced its Internship Program in 2009. The Internship Program is committed to providing access to computational biology training, especially for students from developing regions, and improving competencies in the field. Here, we present how the Internship Program works and the impact of the internship opportunities so far, along with the challenges associated with this program.

2017 ISCB Innovator Award: Aviv Regev.

2017 marks the second year of the International Society for Computational Biology (ISCB) Innovator Award, which recognizes an ISCB scientist who is within two decades of having completed his or her graduate degree and has consistently made outstanding contributions to the field. The 2017 winner is Dr. Aviv Regev, Professor of Biology at the Massachusetts Institute of Technology (MIT), a Core Member and Chair of the Faculty of the Broad Institute of MIT and Harvard, and an HHMI Investigator. Regev will receive her award and deliver a keynote address during International Conference on Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB) 2017 in Prague, Czech Republic (July 21 - 25, 2017).

2017 Outstanding Contributions to ISCB Award: Fran Lewitter.

The Outstanding Contributions to the International Society for Computational Biology (ISCB) Award was launched in 2015 to recognize individuals who have made lasting and valuable contributions to the Society through their leadership, service, and educational work, or a combination of these areas. Fran Lewitter is the 2017 winner of the Outstanding Contributions to ISCB Award and will be recognized at the 2017 Intelligent Systems for Molecular Biology (ISMB)/European Conference on Computational Biology, meeting in Prague, Czech Republic being held from July 21-25, 2017.

The International Society for Computational Biology and WikiProject Computational Biology: celebrating 10 years of collaboration towards open access

The International Society for Computational Biology and WikiProject Computational Biology: celebrating 10 years of collaboration towards open access

Message from the ISCB: 2017 Outstanding Contributions to ISCB Award Given to Fran Lewitter.

Message from the ISCB: 2017 Outstanding Contributions to ISCB Award Given to Fran Lewitter.

A report on the “International Society for Computational Biology - Latin America (ISCB-LA)” Bioinformatics Conference 2016

The fourth edition of the “International Society for Computational Biology - Latin America (ISCB-LA)” Bioinformatics Conference, jointly organised with the Argentine Association for Bioinformatics and Computational Biology (A 2 B 2 C), was held in Buenos Aires, Argentina, on November 2016. The ISCB-LA 2016 conference aimed at showcasing the latest findings in the field from researchers at all career levels in the region and beyond, and promoting collaborations to further develop Bioinformatics and Computational Biology in Latin America. Here we present a brief report on the main activities held during the Conference and their successful outcomes.

A report on the “International Society for Computational Biology - Latin America (ISCB-LA)” Bioinformatics Conference 2016

A report on the “International Society for Computational Biology - Latin America (ISCB-LA)” Bioinformatics Conference 2016

Message from the ISCB: The 5th ISCB Wikipedia competition: coming to a classroom near you?

Message from the ISCB: The 5th ISCB Wikipedia competition: coming to a classroom near you?

2016 ISCB Overton Prize awarded to Debora Marks.

The International Society for Computational Biology (ISCB) recognizes the achievements of an early- to mid-career scientist with the Overton Prize each year. The Overton Prize was established to honor the untimely loss of Dr. G. Christian Overton, a respected computational biologist and founding ISCB Board member. Winners of the Overton Prize are independent investigators in the early to middle phases of their careers who are selected because of their significant contributions to computational biology through research, teaching, and service. 2016 will mark the fifteenth bestowment of the ISCB Overton Prize.  ISCB is pleased to confer this award the to Debora Marks, Assistant Professor of Systems Biology and director of the Raymond and Beverly Sackler Laboratory for Computational Biology at Harvard Medical School.

Program Bytes - Satellite Meetings, SIGs, and AKEs at ISMB 2016.

The International Society for Computational Biology (ISCB) is gearing up for its flagship meeting, ISMB.  The conference is the world’s largest gathering of computational biology and bioinformatics researchers. The ISMB 2016 pre-conference program will feature 17 special interest group and satellite meetings over the course of two days. This article previews those special meetings at ISCB’s flagship meeting, ISMB.

ISMB 2016 offers outstanding science, networking, and celebration.

The annual international conference on Intelligent Systems for Molecular Biology (ISMB) is the major meeting of the International Society for Computational Biology (ISCB). Over the past 23 years the ISMB conference has grown to become the world's largest bioinformatics/computational biology conference. ISMB 2016 will be the year's most important computational biology event globally. The conferences provide a multidisciplinary forum for disseminating the latest developments in bioinformatics/computational biology. ISMB brings together scientists from computer science, molecular biology, mathematics, statistics and related fields. Its principal focus is on the development and application of advanced computational methods for biological problems. ISMB 2016 offers the strongest scientific program and the broadest scope of any international bioinformatics/computational biology conference. Building on past successes, the conference is designed to cater to variety of disciplines within the bioinformatics/computational biology community.  ISMB 2016 takes place July 8 - 12 at the Swan and Dolphin Hotel in Orlando, Florida, United States. For two days preceding the conference, additional opportunities including Satellite Meetings, Student Council Symposium, and a selection of Special Interest Group Meetings and Applied Knowledge Exchange Sessions (AKES) are all offered to enable registered participants to learn more on the latest methods and tools within specialty research areas.

Message from the ISCB: 2016 Outstanding Contributions to ISCB Award: Burkhard Rost.

Message from the ISCB: 2016 Outstanding Contributions to ISCB Award: Burkhard Rost.