{"id":63995,"date":"2023-11-15T10:00:00","date_gmt":"2023-11-15T09:00:00","guid":{"rendered":"https:\/\/www.embl.org\/news\/?post_type=embletc&p=63995"},"modified":"2023-11-15T10:09:56","modified_gmt":"2023-11-15T09:09:56","slug":"embracing-the-genome-sequencing-revolution","status":"publish","type":"embletc","link":"https:\/\/www.embl.org\/news\/embletc\/issue-101\/embracing-the-genome-sequencing-revolution\/","title":{"rendered":"Embracing the genome sequencing revolution"},"content":{"rendered":"\n

DNA is essentially a long thread of genetic code that can be deciphered to access the fundamental instructions for life. In the late 1970s, British scientist Frederick Sanger developed a pioneering method for DNA sequencing \u2013 a breakthrough that earned him his second Nobel Prize in Chemistry in 1980. Ten years after this breakthrough, an international team of scientists set out to sequence all 3 billion letters of the human genome, launching the Human Genome Project. In 2003, two years ahead of schedule, the ambitious goal was reached, and the human genome was sequenced to 99.99% accuracy. By 2007, older sequencing technologies were supplanted by newer methods, collectively called next-generation sequencing, greatly expanding the scope of genomics research.<\/p>\n\n\n\n

The EMBL Genomics Core Facility, also known as GeneCore, has lived through this revolution in the field of genomics. The facility started out in 2001 as a Sanger sequencing provider, under the aegis of biochemist Vladimir Benes, who still leads the facility today. Twenty-two years later, it has evolved into an advanced next-generation sequencing platform. <\/p>\n\n\n\n

The GeneCore team<\/a> currently consists of five research technicians, three bioinformaticians, two senior engineers, and several visiting fellows and associates, who are dedicated to supporting researchers across EMBL’s member states. In addition to providing a wide array of advanced genomics services, the facility serves as a vital resource, facilitating groundbreaking research and fostering scientific innovation. <\/p>\n\n\n\n

\"Two
Ferris Jung, Senior Engineer of NGS Automation and Laura Villacorta, Research Technician, with the liquid handling robot used for automated preparation of NGS libraries. Credit: Stuart Ingham\/EMBL<\/figcaption><\/figure>\n\n\n\n

At its core, the facility specialises in providing genomics technologies, with a primary focus on sequencing techniques. The platform is well-versed in the latest advancements, including what is commonly referred to as next-generation high-throughput sequencing or more accurately, massively parallel sequencing (MPS).<\/p>\n\n\n\n

\u201cThe GeneCore team provides a complete service, from library preparation to sequencing. Beyond the regular services, Vladimir and colleagues are also helpful in developing methods where none exists,\u201d said Ramesh Pillai, Professor at the University of Geneva, Switzerland, and one of GeneCore\u2019s users. <\/p>\n\n\n\n

Another strength of GeneCore is its significant reach within the scientific community in EMBL\u2019s member states. This vast network of users underscores the facility’s importance and its role as a central hub for genomics research. \u201cWe are here to help people flourish in their genomics projects, and this is an element which we believe makes us stronger as a service facility,\u201d said Benes.<\/p>\n\n\n\n

\"A
Daphne Welter, Research Technician monitoring the performance of the Illumina sequencer analysing NGS libraries. Credit: Stuart Ingham\/EMBL<\/figcaption><\/figure>\n\n\n\n

Enabling diverse user projects \u2013 from COVID-19 to the flu virus<\/strong><\/h2>\n\n\n\n

Over the course of its two decades in operation, GeneCore has made significant contributions to a diverse range of projects. <\/p>\n\n\n\n

In 2020, following the outbreak of COVID-19, scientists sequenced the genome of the SARS-CoV-2 virus, creating a significant impact on the global response to the pandemic. GeneCore played its part here, both in the development of tests for diagnostics and in the monitoring of variants. \u201cWhen the pandemic reached us, we were able to pretty quickly set up testing schemes for EMBL,\u201d said Benes. \u201cWe also participated in the sequencing of positive samples from PCR analysis for the identification of SARS-CoV-2 variants of concern. And even there, we were prepared, which is one of GeneCore\u2019s assets.\u201d<\/p>\n\n\n\n

Another example is a long-standing collaboration with Stephen Cusack, former Head of EMBL Grenoble, who has been studying the influenza virus for more than 30 years, contributing to one of the most detailed descriptions of the influenza virus\u2019s RNA polymerase. \u201cCusack\u2019s group created an artificial system to unveil the influenza virus polymerase function, which needed sequencing experiments to be verified,\u201d said Benes. \u201cThey came to us and we helped them solve it. We make sure to take on every project with the same degree of commitment.\u201d<\/p>\n\n\n\n

\"Two
Hilal Ozgur and Mireia Osuna Lopez, Research Technicians in the GeneCore team, using the high-resolution electrophoresis Femto instrument to check the DNA samples’ integrity prior to their processing for long-read sequencing. Credit: Stuart Ingham\/EMBL<\/figcaption><\/figure>\n\n\n\n

\u201cThe GeneCore team has played a central role in advancing the success of my PhD project, notably by establishing tailored capture protocols to investigate the structure of the inactive X chromosome,\u201d said Antonia Hauth, PhD student in the Heard Group at EMBL. \u201cIt is invaluable to have such experts at EMBL, whom we can always directly reach and who have extensive expertise in many (if not all) sequencing-based experiments you could wish for.\u201d  <\/p>\n\n\n\n

GeneCore manages an impressive volume of samples, with approximately 20,000 currently in its care, encompassing both physical specimens and data. Of these, a remarkable 10,000 samples undergo various processing methods to make them suitable for sequencing, underscoring the facility’s dedication to advancing genomics within the EMBL research community.<\/p>\n\n\n\n

Democratising model organism research and handling data<\/strong><\/h2>\n\n\n\n

Genomics technologies have advanced significantly in recent years, becoming increasingly faster and more efficient. Modern sequencers, like those based on Illumina’s technology, can generate millions to billions of DNA sequences in a single run, producing terabytes of data in a matter of hours. As of today, some of the fastest high-throughput DNA sequencers can sequence the DNA of a human-sized genome (approximately 3 billion base pairs) in a matter of hours to a day. <\/p>\n\n\n\n

\u201cWe get every kind of organism, from all sorts of bacteria, fish, mice, and human samples. A couple of years ago the concept of model organisms was very biased due to their historically accessible features. With sequencing, you can have your own model organism\u201d said Benes. \u201cNext-generation sequencing has, in a way, democratised this space, by opening up access to the primary information which every organism has \u2013 the genome.\u201d <\/p>\n\n\n\n

Beyond the provision of cutting-edge technology, GeneCore actively assists researchers in taking their genomics projects to completion, ensuring they receive the guidance and support needed for success. With an end-to-end service, the facility guides the users from the experimental design to the final data analysis and interpretation of results.<\/p>\n\n\n\n

\u201cGenecore has helped me to fully understand the technicalities behind my sequencing projects and this has greatly improved the quality and throughput of my work,\u201d said Carlos Voogdt, EIPOD Postdoctoral fellow in the Zimmermann, Typas, and Zeller groups. \u201cWith their expertise and patience, they are also assisting us in the generation of high-quality whole-genome sequences of hundreds of bacterial strains.\u201d<\/p>\n\n\n\n

\u201cThe dedication of the Genecore Team leads to high-quality data that is fundamentally supporting our research questions,\u201d said Matthias Gro\u00df, Research Technician in the Zimmermann Group at EMBL Heidelberg. <\/p>\n\n\n\n

GeneCore also supports scientists in managing the impressive data volumes that come out of sequencing experiments \u2013 one single DNA sequencing run can produce data comparable to the amount of text found in more than 1 million average-sized novels, assuming each base sequenced corresponds to a letter in a book.<\/p>\n\n\n\n

\u201cTo date, GeneCore has generated more than 100 terabases of MPS sequence data for its users,\u201d said Benes. \u201cSuch data volumes can be overwhelming, and for sure, we need to interpret them, and this requires a very intimate interaction with the users. That\u2019s why GeneCore is also equipped with computational biologists and bioinformaticians. On top of that, we also train the users to interpret their own data. It\u2019s one of GeneCore\u2019s priorities to provide guidance throughout experiments.\u201d<\/p>\n\n\n\n

\"Four
GeneCore sequencing room, with Illumina Sequencers running; their powerful suite provides users with adequate flexibility and throughput to meet their needs timely. Credit: Stuart Ingham\/EMBL<\/figcaption><\/figure>\n\n\n\n

Looking ahead: the future of genomics<\/strong><\/h2>\n\n\n\n

According to Benes, genomic sequencing of cancer cells is one of the key topics destined to be more and more relevant in the future. \u201cThere\u2019s no question that genomics will help substantially in cancer research. There are also many other diseases with genetic underpinnings, and sometimes the detail is incredibly small \u2013 like single base mutations in the DNA. This is not very easy to find, and GeneCore helps find these tiny hallmarks in genomes,\u201d he said. \u201cThe refinement of sequencing methods will also continue to advance rapidly.\u201d The facility is also poised to provide significant support for TREC Traversing European Coastlines (TREC), the flagship project of EMBL\u2019s Planetary Biology<\/a> transversal theme.<\/p>\n\n\n\n

\u201cWe\u2019re seeing TREC samples coming into the facility already,\u201d said Benes. \u201cOur contribution to the project revolves around single-cell transcriptomics and DNA barcoding.\u201d For example, in collaboration with Flora Vincent, Group Leader at EMBL Heidelberg, the GeneCore team helped optimise the method for direct DNA barcoding, eliminating the need for DNA isolation. <\/p>\n\n\n\n

Furthermore, working alongside Rainer Pepperkok, Director of Scientific Core Facilities and Services, EMBL, and Johan Decelle, Junior Group Leader at CNRS, the team will be spearheading single-cell transcriptome analysis.<\/p>\n\n\n\n

\u201cThe GeneCore team is also putting great effort into reducing waste as much as possible,\u201d said Gro\u00df. \u201cTheir offer to share a number of instruments and train users for those could serve as a role model for many other institutes all over Germany to become more sustainable.’<\/p>\n\n\n\n

In a time defined by extraordinary progress in genomics and its maturing tools, Benes and the GeneCore team at EMBL will continue to shape the way we think about science and address global challenges.<\/p>\n\n\n\n

\u201cSequencing always brings the element of surprise, as it often uncovers unexpected findings, and this sense of discovery is what makes running the platform so exciting,\u201d concluded Benes.<\/p>\n","protected":false},"excerpt":{"rendered":"

EMBL\u2019s Genomics Core Facility provides end-to-end support to researchers across Europe and beyond and stands at the forefront of scientific breakthroughs.<\/p>\n","protected":false},"author":159,"featured_media":64033,"parent":0,"menu_order":0,"template":"","tags":[227,386,42,11419,491],"class_list":["post-63995","embletc","type-embletc","status-publish","has-post-thumbnail","hentry","tag-core-facility","tag-genecore","tag-genomics","tag-services","tag-single-cell-genomics"],"acf":{"featured":true,"show_featured_image":false,"field_target_display":"embl","field_article_language":{"value":"english","label":"English"},"article_intro":"

EMBL\u2019s Genomics Core Facility provides end-to-end support to researchers across Europe and beyond and stands at the forefront of scientific breakthroughs.<\/p>\n","related_links":[{"link_description":"EMBL Genomics Core Facility (GeneCore)","link_url":"https:\/\/www.embl.org\/groups\/genomics\/"}],"source_article":false,"in_this_article":false,"press_contact":"None","article_translations":false,"languages":"","embletc_issue":[{"ID":63969,"post_author":"72","post_date":"2023-11-15 10:00:00","post_date_gmt":"2023-11-15 09:00:00","post_content":"","post_title":"Issue 101","post_excerpt":"","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"issue-101","to_ping":"","pinged":"","post_modified":"2024-05-29 12:02:08","post_modified_gmt":"2024-05-29 10:02:08","post_content_filtered":"","post_parent":0,"guid":"https:\/\/www.embl.org\/news\/?post_type=embletc-issue&p=63969","menu_order":0,"post_type":"embletc-issue","post_mime_type":"","comment_count":"0","filter":"raw"}],"embletc_in_this_issue":[{"ID":63997,"post_author":"96","post_date":"2023-11-15 10:00:00","post_date_gmt":"2023-11-15 09:00:00","post_content":"\n

How do cells eat? This question lies at the focus of research undertaken by the L\u00f6w Group<\/a> at EMBL Hamburg<\/a> and Centre for Structural Systems Biology (CSSB)<\/a>. Using structural biology methods, they explore how \u2018promiscuous\u2019 proteins enable cells to absorb nutrients, and how this could be used to make drug uptake more efficient in the future.<\/p>\n\n\n\n

Promiscuity has more to do with nutrition than you think<\/strong><\/h2>\n\n\n\n

To survive, living cells absorb nutrients from their environment. Their menu includes various delicacies, such as sugars, fats, and peptides, which are tiny pieces of digested proteins that cells use to build their own proteins. To capture and pull these nutrients inside, cells use dedicated transporter molecules that sit in the cell membrane.<\/p>\n\n\n\n

Many molecular transporters are highly specialised, e.g. they only transport one type of sugar. But it\u2019s different for peptides \u2013 and that\u2019s where promiscuity comes into play.<\/p>\n\n\n\n

Peptide transporters known as POTs (proton-coupled oligopeptide transporters) are not picky at all. In fact, they\u2019ll grab almost any peptide they find in their way, regardless of its composition and shape. This ability is described by structural biologists as \u2018promiscuity\u2019.<\/p>\n\n\n\n

\u201cHow promiscuity works has been one of the main questions in structural biology,\u201d said Christian L\u00f6w, Group Leader at EMBL Hamburg<\/a> and Centre for Structural Systems Biology (CSSB)<\/a>. \u201cPOTs are especially fascinating, because they are much more promiscuous than most other transporters. You could compare them to a lock that can be opened by many different keys. I wanted to learn how this works.\u201d<\/p>\n\n\n\n

The L\u00f6w Group are experts in structural biology of membrane proteins, in particular promiscuous nutrient transporters. Their work on different POTs, ranging from those in bacteria to those in humans, has yielded many insights that may help solve the mystery.<\/p>\n\n\n\n

A vehicle that wraps itself around the passenger<\/strong><\/h2>\n\n\n\n

The L\u00f6w Group explored this further in their recent work in collaboration with the Marquez Team<\/a> at EMBL Grenoble and the Steyaert Lab<\/a> at the Vrije Universiteit Brussel. They determined and compared the X-ray structures of a bacterial POT called DtpB while it was bound to 14 dietary peptides<\/a> of different sizes, shapes, and chemical properties. They were surprised to see that during the transport, DtpB undergoes major structural changes to adapt itself to each peptide, while the structure of the peptides themselves remains largely unchanged.<\/p>\n\n\n\n

\u201cYou could compare it to a vehicle that wraps itself around the passenger to transport them. In the world of molecular biology, this is very counterintuitive,\u201d said L\u00f6w.<\/p>\n\n\n\n

Further experiments brought more surprises as they showed that the peptides that most strongly bind to DtpB are poorly transported. The peptides transported most efficiently were actually the ones with moderate binding strength.<\/p>\n\n\n\n

\u201cStrong binding is like superglue that gets the peptides stuck inside DtpB and block the passage for other peptides,\u201d said Katharina Jungnickel, postdoc in the L\u00f6w Group.<\/p>\n\n\n\n

This pattern most likely also applies to POTs in humans and other species, such as those that transport dietary peptides from the gut into the bloodstream \u2013 which the L\u00f6w Group studied as well<\/a>. In fact, the scientists expect that \u2018moderate binders are best\u2019 could be a more general feature of promiscuous transporters across organisms.<\/p>\n\n\n\n

POTs can be found in different organisms and cell types. For example, in the human gut, the POT called Peptide Transporter 1 (PepT1) enables the uptake of dietary peptides as well as many drugs, including antibiotics and antivirals. The structure of PepT1 in the image is based on the PDB entries: 7PMW<\/a>, 7PMX<\/a>, 7PMY<\/a> and 7PN1<\/a>. Credit: Isabel Romero Calvo\/EMBL<\/figcaption><\/figure>\n\n\n\n

Promiscuity informs drug design<\/strong><\/h2>\n\n\n\n

Understanding POTs\u2019 promiscuity may be key for improving drug design.<\/p>\n\n\n\n

POTs transport many peptide-like drugs. For example, in the human gut, POTs are responsible for the uptake of various drug molecules, e.g. some drugs for hypertension, while in bacteria, they may serve as an entry point for certain antibiotics.<\/p>\n\n\n\n

However, this transport is often inefficient, so high drug doses are needed. This in turn may cause more side effects. Many potentially effective drugs might not even get transported to the right places in the body. This is one among several reasons why drugs fail in clinical trials.<\/p>\n\n\n\n

\u201cIf we could predict which drugs will be transported at early stages of drug development, this would save a lot of time and money,\u201d said Vadim Kotov, former postdoc in the L\u00f6w Group, now working in industry. \u201cThat\u2019s why we tried to crack the code that determines which peptides gets transported.\u201d<\/p>\n\n\n\n

To pursue this, the scientists combined experiments with machine learning. To their surprise, the analysis revealed that DtpB is much less promiscuous than thought before \u2013 out of the 8400 possible di- and tripeptides, it is likely to bind only a few hundred. They also identified a few factors, such as peptide size, charge and chemical properties, that are key for peptide recognition.<\/p>\n\n\n\n

Using this information, the scientists have built a bioinformatics pipeline that could be used for other POTs to predict which peptides might potentially get transported and which definitely not. Eventually, this could help the pharmaceutical industry exclude poorly absorbed drugs at earlier stages of drug development. However, for more precise predictions, more research is necessary.<\/p>\n\n\n\n

\u201cIt\u2019s still a mystery what exactly the peptides need in order to be transported,\u201d said Jungnickel. \u201cAlthough it\u2019s a relatively simple system, it\u2019s harder to figure out than we thought.\u201d<\/p>\n\n\n\n

\u201cArguably, an even larger dataset would be necessary to train next-generation predictive models,\u201d added Kotov.<\/p>\n\n\n\n

A 2-in-1 molecule<\/strong><\/h2>\n\n\n\n

Another recent study by the L\u00f6w Group in collaboration with colleagues from Boehringer Ingelheim dives into the function of another POT, called PHT1 (peptide\/histidine transporter 1). It is found in the membrane of lysosomes, cell organelles involved in \u2018digesting\u2019 defective and worn-out cellular components, among other functions. PHT1 is quite peculiar because besides transporting peptides, it can also detect signals and trigger molecular reactions inside the cell. Proteins with this ability are called receptors.<\/p>\n\n\n\n

\u201cWe never expected that PHT1 could function as a receptor,\u201d said T\u00e2nia Cust\u00f3dio, postdoc in the L\u00f6w Group. \u201cPOTs are predicted to have similar transport mechanisms and having a dual transport-receptor function was unheard of. I was really curious to understand the function of this peptide transporter in our immune system.\u201d<\/p>\n\n\n\n

While PHT1 is important for our immunity, overactivity of its receptor function may lead to autoimmune diseases, such as systemic lupus erythematosus, as well as to inflammatory bowel diseases and type 2 diabetes. Blocking PHT1 receptor function might, therefore, help treat systemic lupus erythematosus.<\/p>\n\n\n\n

Designing such blocker molecules requires knowing the detailed structure of PHT1. To enable this, the L\u00f6w Group determined the molecular structure of PHT1 and mapped its interaction surface with another protein that helps PHT1 to trigger the molecular response to signals.<\/p>\n\n\n\n

This model can serve as a guide for other researchers to develop molecules that would either block peptide transport or the receptor function of PHT1.<\/p>\n\n\n\n

<\/a>\u201cTen years of POT research at EMBL \u2013 from bacteria to humans and back \u2013 during which we obtained fantastic molecular insights into the structure and mechanisms of this important transporter family,\u201d said L\u00f6w. \u201cThe research opens up new avenues in academic settings and pharmaceutical industry. Our findings can be used to modify existing and future drugs for improved uptake or to develop small molecules to inhibit the PHT1\u2019s receptor function. The future looks bright for transporter research.\u201d<\/p>\n","post_title":"The secret of molecular promiscuity","post_excerpt":"Promiscuity is critical for nourishment. How? This question lies at the focus of research by the L\u00f6w Group at EMBL Hamburg. Using structural biology methods, they explore how specialised molecules located in the cell membrane allow cells absorb nutrients from their environment.","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"the-secret-of-molecular-promiscuity","to_ping":"","pinged":"","post_modified":"2023-11-21 15:01:40","post_modified_gmt":"2023-11-21 14:01:40","post_content_filtered":"","post_parent":0,"guid":"https:\/\/www.embl.org\/news\/?post_type=embletc&p=63997","menu_order":0,"post_type":"embletc","post_mime_type":"","comment_count":"0","filter":"raw"},{"ID":64001,"post_author":"77","post_date":"2023-11-15 10:00:00","post_date_gmt":"2023-11-15 09:00:00","post_content":"\n

In a world inundated with data, curating valuable information has never been more challenging, or more important. From academic papers to scientific databases, the deluge of new information can be overwhelming, leaving researchers in a constant struggle to keep up. However, a groundbreaking innovation in artificial intelligence is helping to transform the data curation landscape: large language models (LLMs) such as those behind ChatGPT. Powered by sophisticated deep-learning algorithms, these models are revolutionising how we streamline and curate massive volumes of data.<\/p>\n\n\n\n

Here we look at some of the ways researchers at EMBL\u2019s European Bioinformatics Institute (EMBL-EBI) are taking advantage of LLMs to aid their data curation processes. From automating the summary and annotation of academic papers to assisting with ontology mapping, LLMs are not just aiding human curators but also have the potential to enhance the quality of the data EMBL-EBI provides to its users. <\/p>\n\n\n\n\n\n

Transforming data curation <\/strong><\/h2>\n\n\n\n

Academic papers are currently being published at an unprecedented pace, and the challenge of pulling out relevant information has never been greater. Andrew Green, ARISE Fellow at EMBL-EBI<\/a> has been using LLMs to streamline the data curation for EMBL-EBI\u2019s database for non-coding RNAs, RNAcentral<\/a>. <\/p>\n\n\n\n

To do this, Green has successfully developed a tool to scrape scientific articles that mention specific RNA identifiers. These sentences are then fed into GPT-3.5, which generates concise, coherent summaries about the RNA of interest. These summaries describe key details such as the RNA's functions, its involvement in diseases, and the organisms in which it has been studied.<\/p>\n\n\n\n

\"One of the intriguing features of using LLMs is the accuracy and contextual understanding they bring into the summarisation process,\" said Green. \"We've seen the model accurately decipher acronyms in a given context and even self-correct its errors when asked to fact-check its summaries.\"<\/p>\n\n\n\n

To ensure the summaries generated are robust, they go through multiple rounds of validation, and are then rated for quality before appearing in the RNAcentral database. The summaries serve as quick references for scientists to better understand a particular RNA, and also include clickable citations to the original articles on Europe PMC<\/a>.<\/p>\n\n\n\n

\"It's crucial to remember that LLMs don't inherently know the difference between what's real and what's fabricated,\u201d added Green. \u201cIn the scientific community, where factual accuracy is paramount, this could be a major concern. Models can sometimes 'hallucinate' details that aren't in the original text. To mitigate this, we have put multiple validation rounds in place. This, combined with constant human oversight, ensures that the information presented is both accurate and reliable.\"<\/p>\n\n\n\n

At the heart of this approach is an automated method for extracting and summarising valuable information from a multitude of academic articles. This means that this work can also be applied to many other EMBL-EBI resources. Once fully developed and implemented, this automated process for curation serves to aid the work of many of EMBL-EBI\u2019s curators, acting as a first filter in the lengthy process of data collection and interpretation. <\/p>\n\n\n\n

Accelerating annotation <\/strong><\/h2>\n\n\n\n

Another aspect of the EMBL-EBI database pipelines that can benefit from LLMs is data annotation. Melanie Vollmar is an ARISE Fellow at EMBL-EBI<\/a> with a strong background in structural biology and a growing expertise in machine learning. As part of her fellowship, she is looking at how to fully automate the extraction of functional information about proteins from academic papers using LLMs. <\/p>\n\n\n\n

Her project focuses on gathering structural information from the Protein Data Bank in Europe (PDBe) and supplementing it with related academic publications from Europe PMC. This curated information is then mined for specific functional details, which are mapped back onto the protein sequences listed in UniProt<\/a>. <\/p>\n\n\n\n

Until now, curating literature for functional annotations followed a purely manual approach supplemented by traditional text mining methods. LLMs, designed to grasp the intricacies of human language, can parse through vast amounts of scientific literature, weigh contrasting opinions, and generate complex text-based outputs. <\/p>\n\n\n\n

This capability can bring in a new era of data enrichment, as these models help to extract more detailed and contextually rich information from existing biological literature at an accelerated pace. At no point is such a model intended to replace the human biocurator who is required to provide a critical view on the produced output.<\/p>\n\n\n\n

\u201cWith automation, not only do we increase the pace at which we can annotate data, but we also enrich the quality of that data, offering a more comprehensive resource for our users,\u201d said Vollmar. \u201cOur focus now is on protein structures, but the beauty of our approach is its adaptability: the methods we're developing could easily be transplanted onto other types of biological data, elevating the annotation process across the board.\"<\/p>\n\n\n\n

Fine-tuning existing LLMs <\/strong><\/h2>\n\n\n\n

Europe PMC is EMBL-EBI\u2019s home of scientific literature, and after many years of serving the scientific community, the resource remains an intuitive and powerful search tool to help users stay on the cutting edge of science. Many of the database's functionalities rely on literature curation, which involves scanning through dense academic material to extract essential information. <\/p>\n\n\n\n

Santosh Tirunagari, Senior Machine Learning Developer<\/a> at EMBL-EBI is leveraging the capabilities of LLMs to accelerate the curation of scientific literature within Europe PMC. He and others in the team have developed specialised named entity recognition models, which are fine-tuned versions of existing LLMs. These sophisticated tools are designed to automatically identify critical scientific entities such as genes, proteins, diseases, and chemicals in research papers and patents.<\/p>\n\n\n\n

Using this approach helps to side-step the high computational costs of developing a language model from scratch, which could require dozens of GPUs and extensive training time. By concentrating on the fine-tuning phase, Tirunagari has been able to adapt these powerful language models to specific tasks relevant to scientific curation. This maximises efficiency while achieving high levels of accuracy.<\/p>\n\n\n\n

In one of his models, Tirunagari also uses an innovative \u2018human-in-the-loop' methodology for model training. Beginning with a limited dataset, the fine-tuned models undergo further adjustments using additional scientific papers. Human curators then verify the model's findings, enabling an iterative feedback loop that continually improves the model\u2019s accuracy.<\/p>\n\n\n\n

\"Large language models have been a game-changer in our efforts to automate the complex task of scientific curation. By fine-tuning these models, we've been able to develop highly specialised tools that can sift through vast amounts of scientific literature and patents to identify key entities such as genes, organisms, proteins, and diseases with impressive accuracy,\u201d said Tirunagari. \u201cThis not only accelerates our work but also opens up new possibilities for collaborations, like our ongoing partnership with Open Targets to use these models to aid drug discovery.\"<\/p>\n\n\n\n

A novel approach to ontology mapping <\/strong><\/h2>\n\n\n\n

Ontologies are structured, hierarchical classifications that are widely used for standardising diseases. Current practices for ontology mapping rely heavily on manual curation, making it a time-consuming and error-prone task. To address these issues, Kirill Tsukanov, Senior Bioinformatician at EMBL-EBI<\/a>, has developed a new method for ontology mapping using openly-available, GPT-based language models. <\/p>\n\n\n\n\n\n

The new method integrates EMBL-EBI\u2019s Ontology Lookup Service (OLS)<\/a> with GPT-3.5 to evaluate the relevancy of ontology terms provided by OLS. Rather than generating ontology identifiers from scratch, the GPT model is tasked with grading existing mappings. This new workflow enables the system to map about 20% more terms compared to existing methods while retaining the same accuracy.<\/p>\n\n\n\n

\"Our prototype already shows immense promise,\u201d said Tsukanov. \u201cThe integration of GPT models helps us overcome the limitations of existing systems, increasing the speed of ontology mapping. The application of LLMs in our research is not just innovative; it's transformative. These models are helping us bridge the gap between raw, unstructured information and actionable, standardised data.\"<\/p>\n\n\n\n

\"While LLMs like GPT-3.5 have proven to be invaluable in tasks like ontology mapping, they present an intriguing challenge,\u201d continues Tsukanov. \u201cThese models don't inherently know the difference between fact and fiction. Recognising this, we've been careful to integrate additional layers of validation and are exploring the use of open-source, stable models that can be fine-tuned specifically for our ontological needs. The goal is to have a tool that not only understands human language but aligns that understanding with the precise, standardised terms in our ontologies.\"<\/p>\n\n\n\n

The project is currently in its developmental phase but Tsukanov plans to test the stability of other LLMs to further improve this new system. The ultimate goal is to create a universally applicable library, serving as a foundation for ontology mapping for different EMBL-EBI initiatives.<\/p>\n\n\n\n

Large language models: a catalyst for change<\/strong><\/h2>\n\n\n\n

The advent of LLMs such as GPT represents a pivotal moment not only in the field of artificial intelligence but also in how we handle, curate, and understand enormous volumes of data. The success stories above show that, while not without their challenges, LLMs hold immense promise for making our data-rich world more understandable, accessible, and usable.<\/p>\n\n\n\n

There are obstacles to overcome, one of the foremost concerns is data integrity and trustworthiness: as LLMs are trained on massive datasets, there's a risk of perpetuating inaccuracies or biases present in the source data. This is particularly critical in scientific applications where incorrect or biased information could have far-reaching implications. Additionally, the automated nature of LLMs could lead to unintended consequences, such as the omission of nuanced insights that human experts might catch, thereby impacting the quality and reliability of curated data. <\/p>\n\n\n\n

Given these complexities, it's crucial to integrate ethical considerations into the design, implementation, and ongoing management of LLMs in scientific data curation.To address these challenges, our researchers discuss how they have implemented multi-layered verification frameworks for data curated by LLMs. Regular updates to the LLMs themselves, coupled with continuous feedback loops with human curators, allow for ongoing refinement of the models, reducing the likelihood of errors over time.<\/p>\n\n\n\n

As LLMs become an increasingly integral part of scientific research, vigilance in maintaining data quality remains a top priority. As the technology matures and as we get better at integrating human expertise with machine capabilities, these challenges are likely to diminish. Ultimately, LLMs have the potential to act as powerful catalysts in the evolution of data curation and scientific research, propelling us into an era where data can not only inform but also enhance our pursuit of understanding.<\/p>\n","post_title":"Deciphering the data deluge: how large language models are transforming scientific data curation","post_excerpt":"Large language models are changing the way we carry out scientific data curation, annotation, and research, setting the stage for a more efficient understanding of scientific literature\n","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"deciphering-the-data-deluge-how-large-language-models-are-transforming-scientific-data-curation","to_ping":"","pinged":"","post_modified":"2023-11-15 10:09:02","post_modified_gmt":"2023-11-15 09:09:02","post_content_filtered":"","post_parent":0,"guid":"https:\/\/www.embl.org\/news\/?post_type=embletc&p=64001","menu_order":0,"post_type":"embletc","post_mime_type":"","comment_count":"0","filter":"raw"}]},"yoast_head":"\nEmbracing the genome sequencing revolution | EMBL<\/title>\n<meta name=\"description\" content=\"EMBL\u2019s Genomics Core Facility provides end-to-end support to researchers globally and stands at the forefront of scientific breakthroughs.\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.embl.org\/news\/embletc\/issue-101\/embracing-the-genome-sequencing-revolution\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Embracing the genome sequencing revolution | EMBL\" \/>\n<meta property=\"og:description\" content=\"EMBL\u2019s Genomics Core Facility provides end-to-end support to researchers globally and stands at the forefront of scientific breakthroughs.\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.embl.org\/news\/embletc\/issue-101\/embracing-the-genome-sequencing-revolution\/\" \/>\n<meta property=\"og:site_name\" content=\"EMBL\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/embl.org\/\" \/>\n<meta property=\"article:modified_time\" content=\"2023-11-15T09:09:56+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/11\/Genonic-Core-Facitiies_014-Edit-scaled-e1699001050216.jpg\" \/>\n\t<meta property=\"og:image:width\" content=\"1000\" \/>\n\t<meta property=\"og:image:height\" content=\"600\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/jpeg\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:site\" content=\"@embl\" \/>\n<meta name=\"twitter:label1\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data1\" content=\"8 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\/\/www.embl.org\/news\/embletc\/issue-101\/embracing-the-genome-sequencing-revolution\/\",\"url\":\"https:\/\/www.embl.org\/news\/embletc\/issue-101\/embracing-the-genome-sequencing-revolution\/\",\"name\":\"Embracing the genome sequencing revolution | EMBL\",\"isPartOf\":{\"@id\":\"https:\/\/www.embl.org\/news\/#website\"},\"primaryImageOfPage\":{\"@id\":\"https:\/\/www.embl.org\/news\/embletc\/issue-101\/embracing-the-genome-sequencing-revolution\/#primaryimage\"},\"image\":{\"@id\":\"https:\/\/www.embl.org\/news\/embletc\/issue-101\/embracing-the-genome-sequencing-revolution\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/11\/Genonic-Core-Facitiies_014-Edit-scaled-e1699001050216.jpg\",\"datePublished\":\"2023-11-15T09:00:00+00:00\",\"dateModified\":\"2023-11-15T09:09:56+00:00\",\"description\":\"EMBL\u2019s Genomics Core Facility provides end-to-end support to researchers globally and stands at the forefront of scientific breakthroughs.\",\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/www.embl.org\/news\/embletc\/issue-101\/embracing-the-genome-sequencing-revolution\/\"]}]},{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\/\/www.embl.org\/news\/embletc\/issue-101\/embracing-the-genome-sequencing-revolution\/#primaryimage\",\"url\":\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/11\/Genonic-Core-Facitiies_014-Edit-scaled-e1699001050216.jpg\",\"contentUrl\":\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/11\/Genonic-Core-Facitiies_014-Edit-scaled-e1699001050216.jpg\",\"width\":1000,\"height\":600,\"caption\":\"Vladimir Benes, Head of the Genomics Core Facility at EMBL Heidelberg and Jan Provaznik, Bioinformatician in the GeneCore team with the AVITI sequencer, the instrument used for genomic analyses, provided for testing within the framework of collaboration with Element Biosciences. Credit: Stuart Ingham\/EMBL\"},{\"@type\":\"WebSite\",\"@id\":\"https:\/\/www.embl.org\/news\/#website\",\"url\":\"https:\/\/www.embl.org\/news\/\",\"name\":\"European Molecular Biology Laboratory News\",\"description\":\"News from the European Molecular Biology Laboratory\",\"publisher\":{\"@id\":\"https:\/\/www.embl.org\/news\/#organization\"},\"alternateName\":\"EMBL News\",\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":{\"@type\":\"EntryPoint\",\"urlTemplate\":\"https:\/\/www.embl.org\/news\/?s={search_term_string}\"},\"query-input\":{\"@type\":\"PropertyValueSpecification\",\"valueRequired\":true,\"valueName\":\"search_term_string\"}}],\"inLanguage\":\"en-US\"},{\"@type\":\"Organization\",\"@id\":\"https:\/\/www.embl.org\/news\/#organization\",\"name\":\"European Molecular Biology Laboratory\",\"alternateName\":\"EMBL\",\"url\":\"https:\/\/www.embl.org\/news\/\",\"logo\":{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\/\/www.embl.org\/news\/#\/schema\/logo\/image\/\",\"url\":\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2025\/09\/EMBL_logo_colour-1-300x144-1.png\",\"contentUrl\":\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2025\/09\/EMBL_logo_colour-1-300x144-1.png\",\"width\":300,\"height\":144,\"caption\":\"European Molecular Biology Laboratory\"},\"image\":{\"@id\":\"https:\/\/www.embl.org\/news\/#\/schema\/logo\/image\/\"},\"sameAs\":[\"https:\/\/www.facebook.com\/embl.org\/\",\"https:\/\/x.com\/embl\",\"https:\/\/www.instagram.com\/embl_org\/\",\"https:\/\/www.linkedin.com\/company\/15813\/\",\"https:\/\/www.youtube.com\/user\/emblmedia\/\"]}]}<\/script>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Embracing the genome sequencing revolution | EMBL","description":"EMBL\u2019s Genomics Core Facility provides end-to-end support to researchers globally and stands at the forefront of scientific breakthroughs.","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/www.embl.org\/news\/embletc\/issue-101\/embracing-the-genome-sequencing-revolution\/","og_locale":"en_US","og_type":"article","og_title":"Embracing the genome sequencing revolution | EMBL","og_description":"EMBL\u2019s Genomics Core Facility provides end-to-end support to researchers globally and stands at the forefront of scientific breakthroughs.","og_url":"https:\/\/www.embl.org\/news\/embletc\/issue-101\/embracing-the-genome-sequencing-revolution\/","og_site_name":"EMBL","article_publisher":"https:\/\/www.facebook.com\/embl.org\/","article_modified_time":"2023-11-15T09:09:56+00:00","og_image":[{"width":1000,"height":600,"url":"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/11\/Genonic-Core-Facitiies_014-Edit-scaled-e1699001050216.jpg","type":"image\/jpeg"}],"twitter_card":"summary_large_image","twitter_site":"@embl","twitter_misc":{"Est. reading time":"8 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"WebPage","@id":"https:\/\/www.embl.org\/news\/embletc\/issue-101\/embracing-the-genome-sequencing-revolution\/","url":"https:\/\/www.embl.org\/news\/embletc\/issue-101\/embracing-the-genome-sequencing-revolution\/","name":"Embracing the genome sequencing revolution | EMBL","isPartOf":{"@id":"https:\/\/www.embl.org\/news\/#website"},"primaryImageOfPage":{"@id":"https:\/\/www.embl.org\/news\/embletc\/issue-101\/embracing-the-genome-sequencing-revolution\/#primaryimage"},"image":{"@id":"https:\/\/www.embl.org\/news\/embletc\/issue-101\/embracing-the-genome-sequencing-revolution\/#primaryimage"},"thumbnailUrl":"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/11\/Genonic-Core-Facitiies_014-Edit-scaled-e1699001050216.jpg","datePublished":"2023-11-15T09:00:00+00:00","dateModified":"2023-11-15T09:09:56+00:00","description":"EMBL\u2019s Genomics Core Facility provides end-to-end support to researchers globally and stands at the forefront of scientific breakthroughs.","inLanguage":"en-US","potentialAction":[{"@type":"ReadAction","target":["https:\/\/www.embl.org\/news\/embletc\/issue-101\/embracing-the-genome-sequencing-revolution\/"]}]},{"@type":"ImageObject","inLanguage":"en-US","@id":"https:\/\/www.embl.org\/news\/embletc\/issue-101\/embracing-the-genome-sequencing-revolution\/#primaryimage","url":"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/11\/Genonic-Core-Facitiies_014-Edit-scaled-e1699001050216.jpg","contentUrl":"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/11\/Genonic-Core-Facitiies_014-Edit-scaled-e1699001050216.jpg","width":1000,"height":600,"caption":"Vladimir Benes, Head of the Genomics Core Facility at EMBL Heidelberg and Jan Provaznik, Bioinformatician in the GeneCore team with the AVITI sequencer, the instrument used for genomic analyses, provided for testing within the framework of collaboration with Element Biosciences. Credit: Stuart Ingham\/EMBL"},{"@type":"WebSite","@id":"https:\/\/www.embl.org\/news\/#website","url":"https:\/\/www.embl.org\/news\/","name":"European Molecular Biology Laboratory News","description":"News from the European Molecular Biology Laboratory","publisher":{"@id":"https:\/\/www.embl.org\/news\/#organization"},"alternateName":"EMBL News","potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/www.embl.org\/news\/?s={search_term_string}"},"query-input":{"@type":"PropertyValueSpecification","valueRequired":true,"valueName":"search_term_string"}}],"inLanguage":"en-US"},{"@type":"Organization","@id":"https:\/\/www.embl.org\/news\/#organization","name":"European Molecular Biology Laboratory","alternateName":"EMBL","url":"https:\/\/www.embl.org\/news\/","logo":{"@type":"ImageObject","inLanguage":"en-US","@id":"https:\/\/www.embl.org\/news\/#\/schema\/logo\/image\/","url":"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2025\/09\/EMBL_logo_colour-1-300x144-1.png","contentUrl":"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2025\/09\/EMBL_logo_colour-1-300x144-1.png","width":300,"height":144,"caption":"European Molecular Biology Laboratory"},"image":{"@id":"https:\/\/www.embl.org\/news\/#\/schema\/logo\/image\/"},"sameAs":["https:\/\/www.facebook.com\/embl.org\/","https:\/\/x.com\/embl","https:\/\/www.instagram.com\/embl_org\/","https:\/\/www.linkedin.com\/company\/15813\/","https:\/\/www.youtube.com\/user\/emblmedia\/"]}]}},"_links":{"self":[{"href":"https:\/\/www.embl.org\/news\/wp-json\/wp\/v2\/embl-etc\/63995","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.embl.org\/news\/wp-json\/wp\/v2\/embl-etc"}],"about":[{"href":"https:\/\/www.embl.org\/news\/wp-json\/wp\/v2\/types\/embletc"}],"author":[{"embeddable":true,"href":"https:\/\/www.embl.org\/news\/wp-json\/wp\/v2\/users\/159"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.embl.org\/news\/wp-json\/wp\/v2\/media\/64033"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/news\/wp-json\/wp\/v2\/media?parent=63995"}],"wp:term":[{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.embl.org\/news\/wp-json\/wp\/v2\/tags?post=63995"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}