Research Parasite Award

Last updated
The Research Parasite Award
Awarded forOutstanding contributions to the rigorous secondary analysis of data
Hosted byEndowment housed at the University of Pennsylvania
First awarded2017 (2017)
Website https://researchparasite.com/

The Research Parasite Award is an honor given annually at the Pacific Symposium on Biocomputing to recognize scientists who study previously published data in ways not anticipated by the researchers who first generated it. The tongue-in-cheek name of the award refers to a New England Journal of Medicine editorial [1] that coined the term "research parasite" to disparage such work. [2] [3] The idea was first suggested on Twitter by Iowa State University researcher Iddo Friedberg shortly after the editorial was published, [4] and was then brought to life by Casey Greene, a pharmacologist at the University of Pennsylvania. [5]

Contents

Two Research Parasite Awards are given to recognize scientists who have made outstanding and rigorous contributions to analysis of secondary data in biology. Recipients must reuse data generated by someone else to extend, replicate, or disprove a research study in a reproducible manner. The junior parasite award recognizes an outstanding contribution from an early career scientist such as a postdoctoral, graduate, or undergraduate trainee. The senior parasitism award recognizes an individual who has engaged in exemplary research parasitism for a sustained period of time. Since the launch of the award in 2017, [6] a travel grant to attend the Pacific Symposium on Biocomputing has been provided to the junior parasite award winner by GigaScience. [7] Starting for the 2019 award year the awards are supported in part by an endowment housed at the University of Pennsylvania.

Timeline of the creation of the Research Parasite Award. From "Data detectives, self-love, and humility: a research parasite's perspective" by 2019 Junior award winner Claire Duvallet. Research Parasite Award Timeline.jpg
Timeline of the creation of the Research Parasite Award. From "Data detectives, self-love, and humility: a research parasite's perspective" by 2019 Junior award winner Claire Duvallet.

The Research Symbiont Awards, inspired by the Research Parasite Award, was founded by J. Brian Byrd, a physician-scientist at the University of Michigan. [8] Recognizing exemplars in the practice of data sharing, they are given to scientists working in any area of study who have shared data beyond the expectations of their field. [9] Unlike a parasite, naming the data sharing award after symbionts helps stress that this process can be mutually beneficial to the data producing "host" because it increases the scientific impact of their investigators. From 2021 the award has been sponsored by the Wellcome Trust and Dragon Master Foundation. The 2021 winners of the General Symbionts prize were Zhang Yongzhen and Edward C. Holmes for their sharing of the sequence of the first SARSCov2 genome. [10]

Nomination and selection procedures

Recipients self-nominate using a letter that references their published manuscripts that exemplify data reuse in a manner that enhances reproducibility. These published manuscripts should describe original scientific research that involves data re-use, or the secondary analysis of shared data and that extend, replicate, or disprove the results from the original manuscript describing the data.

The nomination materials are reviewed by the Selection Committee, which is made up of at least 3 four-year term positions as well as the past two recipients of the Sustained Parasitism award.

Award laureates

Casey Greene presenting the 2020 award at PSB in Hawaii. ParasiteAwards-PSB-2020.jpg
Casey Greene presenting the 2020 award at PSB in Hawaii.

2017

2018

2019

2020

2021

2022

See also

Related Research Articles

<span class="mw-page-title-main">Joseph DeRisi</span> American biochemist

Joseph Lyman DeRisi is an American biochemist, specializing in molecular biology, parasitology, genomics, virology, and computational biology.

<span class="mw-page-title-main">Pacific Symposium on Biocomputing</span>

The Pacific Symposium on Biocomputing (PSB) is an annual multidisciplinary scientific meeting co-founded in 1996 by Dr. Teri Klein, Dr. Lawrence Hunter and Sharon Surles. The conference is to presentation and discuss research in the theory and application of computational methods for biology. Papers and presentations are peer reviewed and published. PSB brings together researchers from the US and the Asian Pacific nations, to exchange research results and address open issues in all aspects of computational biology. PSB is a forum for the presentation of work in databases, algorithms, interfaces, visualization, modeling, and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology.

<span class="mw-page-title-main">Genomic Standards Consortium</span>

The Genomic Standards Consortium (GSC) is an initiative working towards richer descriptions of our collection of genomes, metagenomes and marker genes. Established in September 2005, this international community includes representatives from a range of major sequencing and bioinformatics centres and research institutions. The goal of the GSC is to promote mechanisms for standardizing the description of (meta)genomes, including the exchange and integration of (meta)genomic data. The number and pace of genomic and metagenomic sequencing projects will only increase as the use of ultra-high-throughput methods becomes common place and standards are vital to scientific progress and data sharing.

SOAP is a suite of bioinformatics software tools from the BGI Bioinformatics department enabling the assembly, alignment, and analysis of next generation DNA sequencing data. It is particularly suited to short read sequencing data.

<i>Biomphalaria straminea</i> Species of gastropod

Biomphalaria straminea is a species of air-breathing freshwater snail, an aquatic pulmonate gastropod mollusk in the family Planorbidae, the ram's horn snails.

<span class="mw-page-title-main">MetaboLights</span>

MetaboLights is a data repository founded in 2012 for cross-species and cross-platform metabolomic studies that provides primary research data and meta data for metabolomic studies as well as a knowledge base for properties of individual metabolites. The database is maintained by the European Bioinformatics Institute (EMBL-EBI) and the development is funded by Biotechnology and Biological Sciences Research Council (BBSRC). As of July 2018, the MetaboLights browse functionality consists of 383 studies, two analytical platforms, NMR spectroscopy and mass spectrometry.

SciCrunch is a collaboratively edited knowledge base about scientific resources. It is a community portal for researchers and a content management system for data and databases. It is intended to provide a common source of data to the research community and the data about Research Resource Identifiers (RRIDs), which can be used in scientific publications. After starting as a pilot of two journals in 2014, by 2022 over 1,000 journals have been using them and over half a million RRIDs have been quoted in the scientific literature. In some respect, it is for science and scholarly publishing, similar to what Wikidata is for Wikimedia Foundation projects. Hosted by the University of California, San Diego, SciCrunch was also designed to help communities of researchers create their own portals to provide access to resources, databases and tools of relevance to their research areas

<i>GigaScience</i> Academic journal

GigaScience is a peer-reviewed scientific journal that was established in 2012. It covers research and large data-sets that result from work in the biomedical and life sciences. The editor-in-chief is Scott Edmunds. Originally, the journal was co-published by BioMed Central and the Beijing Genomics Institute (BGI). In 2016, it left BioMed Central to form a new partnership between the GigaScience Press department of BGI and Oxford University Press. In 2018, GigaScience won the Association of American Publishers' PROSE Award for Innovation in journal publishing in the multidisciplinary category.

<span class="mw-page-title-main">Cospeciation</span> A form of coevolution in which the speciation of one species dictates speciation of another species

Cospeciation is a form of coevolution in which the speciation of one species dictates speciation of another species and is most commonly studied in host-parasite relationships. In the case of a host-parasite relationship, if two hosts of the same species get within close proximity of each other, parasites of the same species from each host are able to move between individuals and mate with the parasites on the other host. However, if a speciation event occurs in the host species, the parasites will no longer be able to "cross over" because the two new host species no longer mate and, if the speciation event is due to a geographic separation, it is very unlikely the two hosts will interact at all with each other. The lack of proximity between the hosts ultimately prevents the populations of parasites from interacting and mating. This can ultimately lead to speciation within the parasite.

<span class="mw-page-title-main">Common Workflow Language</span>

The Common Workflow Language (CWL) is a standard for describing computational data-analysis workflows. Development of CWL is focused particularly on serving the data-intensive sciences, such as Bioinformatics, Medical Imaging, Astronomy, Physics, and Chemistry. A key goal of the CWL is to allow the creation of a workflow that is portable and thus may be run reproducibly in different computational environments.

The Earth BioGenome Project (EBP) is an initiative that aims to sequence and catalog the genomes of all of Earth's currently described eukaryotic species over a period of ten years. The initiative would produce an open DNA database of biological information that provides a platform for scientific research and supports environmental and conservation initiatives. A scientific paper presenting the vision for the project was published in PNAS in April 2018, and the project officially launched November 1, 2018.

<i>Uloborus diversus</i> Species of spider

Uloborus diversus is a species of cribellate orb weaver in the spider family Uloboridae. It is found in the desert regions of the Southwestern United States and Mexico. It is an important model species for understanding the evolution of spidroins and understanding orb-weaving behavior. To provide resources for this research a 2.15-Gbp chromosome-level draft genome assembly was sequenced and assembled to 10 chromosomes.

The Plant Genomics and Phenomics Research Data Repository (PGP) is a data publication infrastructure to comprehensively publish multi-domain plant research data. It is hosted at the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) in Gatersleben, Germany. The repository hosts DOI citeable datasets that are not being published in public repositories because of their volume or data scope. PGP enables the publication of gigabyte-scale datasets and is registered as a research data repository at FAIRSharing.org, re3data.org and OpenAIRE as a valid EU Horizon 2020 open data archive. The above features, the programmatic interface and the support of standard metadata formats, enable PGP to fulfil the FAIR data principles—findable, accessible, interoperable, reusable. The PGP repository was created using the e!DAL software infrastructure and applies an on-premises approach to "bring the infrastructure to the data" (I2D).

<i>Renilla muelleri</i> Species of sea pansy

Renilla muelleri is a species of sea pansy. It has been reported from the Gulf Coast of the United States, notably the Florida panhandle, but is also reported from the eastern coast of South America. It is thought to be a euryhaline littoral species, found to a depth of up to 150 meters.

GigaDB is a disciplinary repository launched in 2011 with the aim of ensuring long-term access to massive multidimensional datasets from life science and biomedical science studies. The datasets are diverse and include genomic, transcriptomic, and imaging data. The datasets are curated by GigaDB biocurators who are employed by BGI and China National GeneBank.

Korean Genome Project (KGP) is the largest Korean Genome Project which currently includes over 10,000 human genomes sequenced in Korea by April 2021. KGP was originated from the national initiative of sequencing the reference Korean and whole population genomes in 2006 by KOBIC, KRIBB and NCSRD, KRISS, Daejeon in Korea. From 2009, KGP was supported by the Genome Research Foundation and TheragenEtex to build the Variome of Koreans as well as the Korean Reference Genome (KOREF). Starting from KOREF, a consensus variome reference, providing information on millions of variants from 40 additional ethnically homogeneous genomes from the Korean Personal Genome Project was completed in 2017. Updating the technology an improved version of KOREF was then constructed using long-read sequencing data produced by Oxford Nanopore PromethION and PacBio technologies has been released showcasing newer assembly technologies and techniques. In 2022 a new chromosome-level haploid assembly of KOREF was published, assembled using Oxford Nanopore Technologies PromethION, Pacific Biosciences HiFi-CCS, and Hi-C technology.

<span class="mw-page-title-main">Zhang Yongzhen</span> Chinese virologist

Zhang Yongzhen, also known as Yong-Zhen Zhang, is a Chinese virologist known for his work relating to the COVID-19 pandemic. A professor at Fudan University, Zhang has discovered numerous RNA viruses and created a network of labs dedicated to monitoring new viruses. He led the team that sequenced and published the genome of SARS-CoV-2, the virus that causes COVID-19, in early January 2020.

<i>Gigabyte</i> (journal) Academic journal


GigaByte is a peer-reviewed open-science journal published by GigaScience Press since 2020. It focuses on short, focused, data-driven articles describing and sharing open research data sets and software. Using an exclusively XML-based publishing system that automates the production process to make it simple to change views, languages and embed interactive content, in 2022 it won the ALPSP Award for Innovation in Publishing.

References

  1. ↑ Longo DL, Drazen JM (January 2016). "Data Sharing". The New England Journal of Medicine. 374 (3): 276–7. doi:10.1056/NEJMe1516564. PMID   26789876.
  2. 1 2 3 Greene CS, Garmire LX, Gilbert JA, Ritchie MD, Hunter LE (March 2017). "Celebrating parasites". Nature Genetics. 49 (4): 483–484. doi:10.1038/ng.3830. PMC   5710834 . PMID   28358134.
  3. ↑ Park Y, Greene CS (November 2018). "A parasite's perspective on data sharing". GigaScience. 7 (11): giy129. doi:10.1093/gigascience/giy129. PMC   6258825 . PMID   30395209.
  4. ↑ Friedberg I (2016-01-22). "I propose a new science award: "The Research Parasite Award is given to those who used someone else's data to do some really cool sh*t"". @iddux. Retrieved 2020-01-06.
  5. 1 2 3 Oransky I, Marcus A. "Congratulations, you're a parasite!" . Retrieved 17 June 2019.
  6. ↑ Altman RB, Dunker K, Hunter A, Ritchie L, Murray T, Klein TE (2016-11-22), Altman RB, Dunker AK, Hunter L, Ritchie MD (eds.), "Preface: Pacific Symposium on Biocomputing 2017", Biocomputing 2017, World Scientific, p. vii, doi:10.1142/9789813207813_fmatter, ISBN   978-981-320-780-6
  7. 1 2 Duvallet C (January 2020). "Data detectives, self-love, and humility: a research parasite's perspective". GigaScience. 9 (1). doi:10.1093/gigascience/giz148. PMC   6940423 . PMID   31897481.
  8. ↑ "The Research Symbiont Awards". researchsymbionts.org. Retrieved 2020-01-11.
  9. ↑ Community Data Science Collective (2019-01-07). "Benjamin Mako Hill is a Research Symbiont!". Community Data Science Collective. Retrieved 2020-01-11.
  10. ↑ "The Research Symbiont Awards". researchsymbionts.org. Retrieved 2021-05-01.
  11. 1 2 "The Research Parasite Awards". researchparasite.com. Retrieved 2020-01-06.
  12. ↑ Callier V. "The Open Data Explosion" . Retrieved 17 June 2019.
  13. ↑ "2019 Research Parasites" . Retrieved 17 June 2019.
  14. ↑ Raman AT (March 2021). "A research parasite's perspective on establishing a baseline to avoid errors in secondary analyses". GigaScience. 10 (3). doi:10.1093/gigascience/giab015. PMC   7953484 . PMID   33710326.
  15. ↑ Nieto, Nicolás; Larrazabal, Agostina; Peterson, Victoria; Milone, Diego H; Ferrante, Enzo (December 2021). "On the relationship between research parasites and fairness in machine learning: challenges and opportunities". GigaScience. 10 (12). doi:10.1093/gigascience/giab086. ISSN   2047-217X. PMC   8685850 . PMID   34927190.
  16. ↑ The 2021 Research Parasite and Symbiont Award Presentation , retrieved 2022-09-17
  17. ↑ Pilgrim, Jack (2022). "The opportunities of research parasitism: A case study using the Barcode of Life Data System (BOLD)". GigaScience. 11. doi:10.1093/gigascience/giac123. ISSN   2047-217X. PMC   9724551 . PMID   36472572.
  18. 1 2 "Vectors of data awards: acknowledging the entire data sharing food web - GigaBlog". gigasciencejournal.com. Retrieved 2022-09-07.
This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.