Defining new criteria for selection of cell-based intestinal models using publicly available databases

Peer reviewe

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

The InterPro database (http://www.ebi.ac.uk/interpro/) classifies protein sequences into families and predicts the presence of functionally important domains and sites. Here, we report recent developments with InterPro (version 70.0) and its associated software, including an 18% growth in the size of the database in terms on new InterPro entries, updates to content, the inclusion of an additional entry type, refined modelling of discontinuous domains, and the development of a new programmatic interface and website. These developments extend and enrich the information provided by InterPro, and provide greater flexibility in terms of data access. We also show that InterPro's sequence coverage has kept pace with the growth of UniProtKB, and discuss how our evaluation of residue coverage may help guide future curation activities

InterPro in 2017-beyond protein family and domain annotations

InterPro (http://www.ebi.ac.uk/interpro/) is a freely available database used to classify protein sequences into families and to predict the presence of important domains and sites. InterProScan is the underlying software that allows both protein and nucleic acid sequences to be searched against InterPro's predictive models, which are provided by its member databases. Here, we report recent developments with InterPro and its associated software, including the addition of two new databases (SFLD and CDD), and the functionality to include residue-level annotation and prediction of intrinsic disorder. These developments enrich the annotations provided by InterPro, increase the overall number of residues annotated and allow more specific functional inferences

FAIR Points: From sdo:LearningResource to FAIR Digital Object

The FAIRPoints organization, co-founded by the authors, aims to provide a platform for conversations to take place around realistic and pragmatic implementations of the FAIR (Findable, Accessible, Interoperable, Reusable) principles. The uniqueness of the FAIRPoints effort stems from an additional aim: to capture conversation contributions in the form of “bite-sized” objects – “points” – in a way that facilitates dynamic composition by instructors for the delivery of audience-customized training experiences. Thus, FAIRPoints aims to cultivate pragmatic learning resources to help realize the FAIR principles in practice, both throughinviting speakers to prime and lead discussions focused on choices/challenges regarding FAIR, andamplifying downstream value potential by serializing “points” made during such events as FAIR resources.Currently, event outcomes are serialized as LearningResource-typed JSON-LD objects in the schema.org sense, i.e. sdo:LearningResource, where @prefix sdo: ., and conform to the bioschemas.org TrainingMaterial profile. However, any differences in participant perspectives must be reconciled, via git revision control, towards a single “view” of a sdo:LearningResource. This situation is at odds with other explicit aims of the FAIRPoints organization such as including diverse voices and collecting heterogeneous input from a global perspective.Using the FAIR Digital Object (FDO) approach, a FAIRPoints sdo:LearningResource instance may be the Object to which an Identifier points, through an FDO Identifier Record, and sdo:LearningResource may be the FDO Type. Crucially, there may be a multiplicity of Metadata records pointed to by an FDO Identifier Record and thus a formal mechanism to cultivate and publish diverse perspectives.This presentation will outline FAIRPoints’ approach to FDO implementation for learning resources and its relation to published practice. Specifically, in relation to the FAIR Digital Twins approach*1, our approach may be seen as the stewardship of a “fluid graph” of learning-resource “knowlets” with support for “qua” projection in service of e.g. an instructor’s dynamic composition of training material for a targeted workshop

<i>"Öppen Vetenskap - </i><i>(ett försök till) Ett helhetsperspektiv" </i>a 10 minutes presentation annotated in Swedish for the conference "Nationellt event om öppen vetenskap och Sveriges engagemang i det europeiska öppna forskningsmolnet (EOSC)"

Öppen Vetenskap - (ett försök till) Ett helhetsperspektiv is a presentation annotated in Swedish presented by Associated Professor Jessica Lindvall (Deputy Head of Node ELIXIR-SE/NBIS, Head of Training SciLifeLab) at the conference "Nationellt event om öppen vetenskap och Sveriges engagemang i det europeiska öppna forskningsmolnet (EOSC)" 12 October 2023 organised by Sveriges universitets- och högskoleförbund (SUHF) and Vetenskapsrådet (VR)The 10 minutes presentation focuses on Open Science from the perspective of Research Infrastructures and outlines initiatives and good examples delivered from SciLifeLab and ELIXIR-SE/NBIS as well as grass root initiatives. It also gives an overview of challenges we believe Research Infrastructures carries today in addition to areas where we believe we can join forces to achieve the goal of Open Science = Science!</p

Solute carriers (SLCs) in cancer

During tumor progression cells acquire an altered metabolism, either as a cause or as a consequence of an increased need of energy and nutrients. All four major classes of macromolecules are affected: carbohydrates, proteins, lipids and nucleic acids. As a result of the changed needs, solute carriers (SLCs) which are the major transporters of these molecules are differently expressed. This renders them important targets in the treatment of cancer. Blocking or activating SLCs is one possible therapeutic strategy. For example, some SLCs are upregulated in tumor cells due to the increased demand for energy and nutritional needs. Thus, blocking them and turning off the delivery of fuel or nutrients could be one way to interfere with tumor progression. Specific drug delivery to cancer cells via transporters is another approach. Some SLCs are also interesting as chemosensitizing targets because blocking or activating them may result in an altered response to chemotherapy. In this review we summarize the roles of SLCs in cancer therapy and specifically their potential as direct or indirect targets, as drug carriers or as chemosensitizing targets. (C) 2012 Elsevier Ltd. All rights reserved

Biospecimens in FDO world

With the advent of technological advances in research settings, scientific collections including sample material became on par with big data. Consequently there is a widespread need to highlight and recognise the inherent value of samples coupled with efforts in unlocking sample potential as resources for new scientific discovery. Samples with informative metadata can be more easily discoverable, more readily shared and reused, allowing reanalysis of associated datasets, avoiding duplicate efforts, and providing metaanalysis yielding considerably enhanced insight. Metadata provides the framework for a consistent, systematic and standardized collection of sample information, enabling users to identify the availability of research output from the samples, relevancy to their intended use, and a way to conveniently identify sample material as well as access provenance information related to the physical samples. Researchers need this essential information aiding their decision making process on the quality, usability and accessibility of the samples and associated datasets. We propose to explore the practical implementation of FAIR Digital Objects (FDO) for biological life science physical samples and practically how to create an FDO framework centralized around biospecimen samples, linked datasets, sample information and PIDs (Persistent Identifiers)Klump et al. 2021. This effort is highly relevant to enhancing the portability of sample information between multiple repositories and other kinds of resources (e.g. e-infrastructures).In this session we would like to present our current work in order to mobilize the community to define the FAIR Digital Object Architecture for biospecimen in life science including all infrastructure components e.g. metadata, PIDs and their integration with technical solutions. To that end, in our community of practice we aim to:What: Identify the minimum set of attributes required for describing biospecimen in biological life science (Minimal Information About a Biological Sample, MIABS) with ontological mapping for semantic unambiguity and machine actionability.Identify the required attributes for registering PIDs for biospecimens and how that will operate in an FDO ecosystem. This will pave the way for a framework of coupling the descriptive metadata to the digital object in a FAIR and comprehensive manner.How:Define a semantic FDO model for biospecimens.Define the role of biospecimen PIDs registration information and kernel attributes and how that translates to machine actionability and programmatic decisions.Define the implementation specifics for integration of biospecimen FDOs with operational infrastructure e.g. e-infrastructures, repositories and machines.Relevant technologies include: RO-Crate, Persistent identifiers, and metadata schemas The recent partnership between IGSN and DataCite described below is a catalyst in this call of action to the FDO community to build a Community of Practice (CoP) specifically focused on biospecimen samples. Community of practice:IGSN e.V. announced a partnership with DataCite, in which DataCite’s registration services and supporting technology for Digital Object Identifiers (another type of PID) are now being leveraged to register IGSN IDs, and thus ensure the ongoing sustainability of the IGSN ID infrastructure. Importantly, the two organizations are also focusing the community’s efforts on advocacy of PIDs for physical samples and expanding the global sample ecosystem. Assisted by the DataCite Samples Community Manager, the IGSN e.V. is establishing working groups (Communities of Practice) within different research domains to support development and promotion of standardized methods for identifying, citing, and locating physical samples. In particular, the partnership wishes to work with the Biosamples community to elaborate the necessary information (metadata) such that those within the community have a full understanding of a physical sample when its descriptive webpage is accessed via its PID, see this example

The role of CDX2 in Caco-2 cell differentiation

Background: CDX2 plays a key part in the differentiation of Caco-2 cells, a colon carcinoma derived cell line that undergoes spontaneous differentiation. The effect of CDX2 expression in Caco-2 cells over time in culture has not been studied yet on a genome-wide level. Methods: The impact of CDX2 expression on the genomic profile of Caco-2 cells was studied by transducing cells with CDX2 targeting shRNAs. Knockdown efficiency was assessed on mRNA level and protein level by RTPCR, microarrays, and Western blots. Gene set enrichment analysis was performed to assess regulation of specific gene sets. Results: CDX2 expression had an inhibitory effect on the transcriptional activity of beta-catenin/TCF at early stages of culturing, while at later stages, its role in the trans-activation of target genes specific for small intestinal enterocytes seemed more dominant. Conclusions: The unique induction of a small intestinal signature upon differentiation in Caco-2 cells seems to be at least partially under the control of CDX2. (c) 2013 Elsevier B.V. All rights reserved