dataesr/scientific-paragraphs-categorization huggingface dataset:
Introduction Biological knowledge data portals (commonly referred to as 'databases' or 'community databases') have been integral resources since the first online research databases were established in the 1990s. These portals often include genetic, genomic, trait and/or breeding data from model organisms, and their continuing and growing importance has been welldescribed in recent reviews by  Oliver et al. (2016)   [1]  and  Leonelli and Ankeny (2012)   [2]. Early trials for agricultural community databases resulted in a handful of successful projects, including MaizeGDB  [3] , CottonDB (CottonGen)  [4]  and Dendrome (TreeGenes)  [5]. Early examples in the biomedical and model organism community included FlyBase  [6] , Wormbase  [7]  and The Arabidopsis Information Resource  [8]. As the need for data integration and community support became evident, online resources for single organisms, taxonomic clades or specific types of data were developed.
Collectively, they enable researchers to access high-quality, curated public data from thousands of research projects. The majority of biological data portals enable data search and exploration through a variety of visualization and analytic tools. Related data are linked or integrated, providing a more complete view of variants, genes, genomes and metabolic networks. For example, many databases offer gene pages that display DNA and RNA sequences, protein products, isoforms, function, orthologs, publications, germplasm, expression data and relevant metabolic networks. With similar use cases, early databases recognized the need for shared software tools and standards, leading to the development and rapid adoption of the Generic Model Organism Database (GMOD;  [9] ). As genomic and phenomic data grow in size and complexity, and as new data types and research methods emerge, individual communities want their own curated repositories.
The requirements of a modern biological data portal far exceeds what any single investigator-led team can accomplish in isolation, even with the support and funding of a larger research community. If individual groups are successful in generating a new database, they must consider how to fund a team of developers to maintain both the framework and data curation activities. Even well-established databases face tremendous challenges when upgrading to new technology platforms, implementing new storage designs (schema modifications) for new data types, and maintaining hardware and software backends. Development of the open source Tripal platform began in 2008 under the auspices of the GMOD project (http://gmod. org/) to address these challenges. Tripal is a generic software platform that provides the means for linking the physical storage of biological information such as genetic, genomic and breeding data to an easy-to-use User Interface (UI) for searching, browsing, loading and curating data  [10] [11] [12].
To enable data curation and site interface management by non-technical staff, it is built on the popular, open source content management system (CMS) Drupal (https://www. drupal. org/). The platform is customizable in appearance and functionality, as well as extendable for each site's unique needs. Tripal supports existing biological standards, including controlled vocabularies, common biological file formats, metadata standards and the standardized object relational database schema, Chado  [13]. Since its inception, Tripal has maintained an active developer community which is recognized as the source of its long-term success. The following will examine the current scope and usage of Tripal, as well as the future development needed to sustain and expand its utility.
Tripal overview Tripal was publicly released in 2009  [10]  and by 2011 had been adopted by at least seven public data portals (Figure  1 ). The current release (version 3. 3) has at least 31 public sites (Table  1 ). Anonymous installation tracking by Drupal reports 130 public instances worldwide  [14, 15]. Tripal supports the Chado data schema  [13]  to house genetic, genomic and breeding data in a Relational Database Management System  [16]. Chado is a part of the GMOD and provides a generic and flexible relational model for complex biological data. It was developed first by FlyBase  [17]  and is used wholly or in part by many data portals today. However, as of Tripal version 3, users can opt to use a different database backend  [12]. The Drupal  [18]  CMS enables contributors without web development experience to build static information pages in Tripal through a simple interface.
This allows users to tailor the look and feel of the website through a page templating system. Drupal provides a wealth of basic functionality such as user authentication, database connectivity and support for community built extension modules, including web-form security, news feeds and event calendars. Drupal has a mature open-source community that continues to maintain, develop and upgrade the platform, including documentation and best practices. All web applications require active security management, and this is particularly critical for sites that have passwordprotected user accounts and private data. Fortunately, Drupal has a dedicated world-wide team of experts focused on security issues with fast turn around and a secure workflow for providing security releases. It is important for Tripal sites to monitor these security updates and keep their Drupal version current.
In contrast, data web portals which do not use a well-established CMS need to handle security concerns on their own. Tripal's modular architecture consists of a set of Drupal modules that provide the building blocks of a biological data portal with built-in web-based content management and display customization. Any biological data store can be tied to Tripal, with support for Chado offered as a built-in option. The Tripal Core module provides functionality required by most biological data portals with a set of centralized services. Tripal's functionality can be extended by building new modules or by extending existing ones. Developers are encouraged to share their modules through the Tripal website (https://tripal. readthedocs. io/en/late st/extensions. html). This architecture provides structure for the member databases and is a key innovation of the Tripal system (Figure  2 ).
Tripal Core provides reliable, centralized services that benefit the majority of member databases, meeting the goals of reducing duplicative development, sharing best practices and exchanging data across community databases. In contrast, the extension modules can accommodate custom development for specific tools or data types. This allows individual databases to develop their own solutions without waiting on the full community for formal approval. Tripal is open source, well-documented and community driven. The primary information portal is http://tripal. info, the Tripal source code and issue queue are available on GitHub (https://github. com/orgs/tripal) and documentation is available via Read the Docs  [16]  (https://tripal. readthedocs. io). Unlike many open source science software projects, Tripal is not coordinated by a single group.
Since the overall goal is to support diverse research groups and database developers with both shared and unique requirements, an open community with strong communication and shared governance is essential. From its inception, the project has maintained an active user and developer community that contributes to Core development, extension module development and community steering. This communication includes monthly meetings, emails, GitHub issues and dedicated Slack channels. Annual codefests have been offered since 2017. To unify the growing international community, a governance structure was established in 2018, consisting of the Tripal Project Management Committee (PMC) and the Tripal Advisory Committee (TAC). This structure was collaboratively designed and the members elected. The PMC are the primary Tripal Core developers, and they guide development that supports the full community.
This is balanced by the TAC, whose membership is largely scientists and principal investigators that are invested in the future of Tripal and its member databases. The responsibilities of these two committees (Figure  3 ) and their communication and voting structures are outlined in the Tripal Community documentation  [16]. The TAC, as implied by the name, acts in an advisory capacity only by providing recommendations for Tripal to the PMC, which can independently make decisions. This structure was designed to ensure Tripal development will be fairly steered to the benefit of all, not any single member database. Since many groups rely on Tripal for the longevity of their databases, Tripal has defined contribution guidelines for Tripal Core. The best practices are outlined in a detailed Developer's Guide and include, for example: Drupal coding standards, GitHub pull request (PR) guidelines and unit testing requirements for new features.
The code is hosted in GitHub and the contribution process is transparent and collaborative. All development, bugs, features and other contributions must start as a GitHub issue to provide the community a chance to comment and review. PRs (i. e. code additions or changes) must link to an issue and be tested by at least two developers. At least one of those developers must be a designated 'trusted committer', who checks that the PR meets the contribution guidelines, provides final approval and merges the modified code into Tripal Core. Extension modules are not governed by the Tripal contribution guidelines, although the community encourages use of the guidelines. To encourage developers to create and maintain extension modules that benefit others, the Tripal community developed a module rating system in 2019.
Updating legacy code and databases To contend with rapid technology changes, biological data portals eventually need to completely upgrade and refactor their code. TreeGenes, previously known as Dendrome when first funded in the early 1990s, recently converted their custom code base to Tripal, providing opportunity to expand to new data types, integrate ontologies and increase biocuration activities. Furthermore, Tripal provided an opportunity to develop a sophisticated web-based application housed within Tree-Genes, CartograTree (https://treegenesdb. org/cartogratree). This resource enables the visualization and analysis of integrated genotype, phenotype and environmental data for georeferenced plants.
Adding breeding data to support growers KnowPuse was established in 2010 for plant breeding, genetic and diversity data for legumes and pioneered support for germplasm, breeding and diversity data in Tripal. Unlike many biological data sites, KnowPulse leverages the power of the Drupal CMS to allow direct update of the resource by contributors. Long-term trusted curators add and edit the database directly, ensuring all users have the most up to date information. KnowPulse is a tangible example of both the ability to support diverse data types and extend Tripal to meet specific community needs.
Supporting many communities for genome access and manual annotation The i5k Workspace@NAL  [23]  supports community curation of genome annotations for over 70 non-model arthropod species. Tripal provided the initial support for housing the emerging genomes, and through a collaboration with another database, the Tripal HQ module was developed to enable community members to submit new data and for the data to undergo review by a database curator prior to acceptance. i5k has recently extended Tripal to link to and exchange data with Apollo, a popular genome annotation tool.
Monitoring quickly emerging genetic variants The United States Swine Pathogen Database (US-SPD: https:// swinepathogendb. org/) is the first centralized data repository for novel and endemic swine pathogens in the USA. Tripal provides a framework to monitor the patterns of genetic change of viruses in swine, enabling researchers to identify possible emerging threats and help control endemic viruses. The database is managed with only one developer yet offers a variety of data types as well as specialized tools, including the ability to classify porcine reproductive and respiratory syndrome virus 2 strains (PRRSV-2) by restriction fragment length polymorphism patterns.
Tripal BLAST: successful collaboration builds a module for everyone The Tripal BLAST extension module (https://github. com/tripal/ tripal_blast/) provides an intuitive UI to the NCBI Blast+ tools  (Camacho et al. , 2009). It features simple installation and integrates with any Drupal theme to ensure it stylistically matches each individual Tripal site. As one of the most installed Tripal extension modules, its ability to be installed on any Tripal site has been well tested and refined. In addition to its popularity, another main success of Tripal BLAST is the community collaboration behind it. The Drupal 7, Tripal 2/3 version of this module was co-developed between the KnowPulse and Legume Federation development teams with sustained collaboration over a couple of years. There has also been substantial community input through both issue reports and PRs with 11 different organizations providing input and five organizations contributing directly to the codebase.
Tripal JBrowse: full integration of an external web application JBrowse is an open source Javascript HTML5 genome browser, developed as a GMOD project, that is fast and scalable (Buels et al. , 2016). The Tripal JBrowse extension module (https://github. com/tripal/tripal_jbrowse) facilitates embedding JBrowse within Tripal sites by providing listings of available JBrowse instances and, optionally, creating pages containing embedded JBrowse instances. This ensures that JBrowse is highlighted within the Tripal site, easily accessible, and facilitates a consistent user experience through shared branding and menus. Tripal JBrowse also provides an administrative interface allowing multiple JBrowse instances to be managed through the Tripal administrative interface. This functionality couples the two web applications and provides a consistent interface to update both Tripal and JBrowse.
Genotype data exploration with Gigwa With the increasing number of genome-wide genotype datasets for large populations, community databases need to not only house this data, but present intuitive filtering and analysis options. The Gigwa application (Genotype Investigator for Genome-Wide Analyses) is an online tool to manage and explore one or more sets of genotypic data  [36]  and supports both the BrAPI (Breeding Application Programming Interface)  [37]  and GA4GH API (Global Alliance for Genomics and Health)  [38]  for programmatic data access. The Tripal Gigwa extension module integrates the features of a Gigwa server into a Tripal site. The administration interface enables data curators or administrators to load data and offers users an interface to select variants by genomic location, gene and variant effect (Figure  5 ).
Cross-site searching with ElasticSearch interlinks community databases Community data portals need to offer a fast, comprehensive keyword search for users; however, including content such as nucleotide sequences is not appropriate for traditional website search engines and leads to both slower performance and nonsensical results. (Sequences should be queried through a specialized algorithm such as the BLAST module described above. ) The Tripal ElasticSearch engine solves this problem by natively integrating with Tripal, allowing a site administrator to use an administrative interface to determine what content to index and what to ignore  [39]. With Tripal version 3, the search results were updated to provide a 'faceted' view that enables users to filter by the type of data. For example, after searching for 'ash', a user could then filter the results to only organism pages or to only gene feature pages.
Drupal Display Suite customizes the look and feel of pages without programming Drupal Display Suite is an extension to Drupal allowing a site manager to take full control over content page display using a drag and drop interface. With this tool, biological data pages can be easily rearranged and styled through the administrative UI without the need to delve into the Drupal templating system. Specifically, concrete pieces of content known as Fields (e. g. gene accession, genomic position, annotations) on a gene page can be moved independently and grouped into HTML div tags, tables, Tripal panes and fieldsets. Tripal extension modules using the Tripal Fields API to provide content automatically integrate with the Drupal Display Suite without any additional programming. This allows content made available by Tripal extension modules to blend seamlessly into an existing biological content page.
Integrating phylogenetics data into Tripal with MSAViewer and Phylotree. js Comparative genomics is a powerful tool for researchers to explore the taxonomic and genomic history of related species. Users need to be able to explore multiple sequence alignments that form the basis for phylogenetic analysis and the resulting trees. Tripal now integrates with existing tools for these tasks: MSAViewer is a full-featured open source Javascript multiple sequence alignment viewer available on sites such as NCBI  [40]   and Phylotree. js is a full-featured Javascript web application used to display phylogenetic trees  [41]  (Figure  7 ). The Tripal MSAViewer and Tripal Phylotree. js extension modules quickly provide UIs to view and analyze alignment and tree data without programming expertise. By leveraging Drupal, the interfaces to these tools can be displayed alongside other content, such as gene, organism and gene family/orthogroup pages, to provide an intuitive user experience.
Breeding Information Management System Breeding programs are producing increasingly large and complex amounts of data. Efficient management systems are needed to keep track of crosses, germplasm, pedigree, performance, geographical and image-based data as well as genotyping data. The Breeding Information Management System (BIMS, https:// www. nrsp10. org/bims) was developed to provide breeders with autonomous control and management of their public or private breeding data in a secure setting. BIMS also allows breeders to integrate public data available in the community database with their private breeding data. BIMS promotes the use and development of standard trait descriptors and metadata. The current functionality includes creating a breeding program, managing user permissions, managing trait/accession/cross/location data, bulk data import/export and individual or bulk data.
Users can compare trait values across multiple datasets and visualize results as graphs with the distribution of the trait values for each dataset and a table with statistical values such as mean, maximum, minimum and standard deviation. The integration of breeding data with publicly available resources, as well as the integration of each breeder's own genotypic and phenotypic data, maximizes the markerassisted breeding utility for breeders and allied scientists. An upcoming version of BIMS will include BrAPI compliance and management of image files.
Sharing standardized breeding information with BrAPI The Breeding API (BrAPI) project aims to enable interoperability among plant breeding databases, genetic databases and end user applications  [37]. It provides a standardized RESTful web service API specification for cross-point communication. The BrAPI Tripal module implements BrAPI specifications to make Tripal sites BrAPI-compliant and has been implemented in MGIS  [27]. It provides an administrative interface to configure each call to match the data storage backend specific to each Tripal site as well as manage user permissions Additional Javascript features allow a Tripal site to query other BrAPI end points and fetch breeding information. As such, the BrAPI Tripal module is a comprehensive solution providing both a secure BrAPI endpoint and a client implementation.
Galaxy module: integration of scientific workflows Biological data portals offer access to very large biological datasets such as RNA/DNA read data or variant calls, but researchers are still faced with the challenges associated with accessing High Performance Computing resources and using the Linux command line. The popular open source analysis workflow system, Galaxy, solves many of these challenges  [42]  by offering an intuitive graphical UI through a web browser for users to select and pipeline software tools. A Tripal Galaxy module is available to link a Tripal site to one or more Galaxy instances  [43]. This enables Tripal sites to offer users sophisticated analysis of large datasets housed by the database and/or with their own datasets. Tripal Galaxy can automatically render a Galaxy workflow as an intuitive web form on a Tripal site.
The user can select datasets from the site or upload their own, alter parameters for each tool in the workflow, then submit the job, all within the 'look and feel' of the Tripal site. The jobs run on the Galaxy server and the results are returned to the user within the Tripal interface. Tripal Galaxy also offers direct access to the Galaxy API via the blend4PHP library  [44]. This can be used by any extension module to call for an analysis job via Galaxy while presenting a customized interface to the user. An example of a module leveraging this approach is Tripal CartograTree  [45]. CartograTree enables users to use a map-based interface to select tree accessions, their associated genotype and/or phenotype data and layers of environmental data. All selected data can be integrated and analyzed by custom landscape genomics and association genomics analysis pipelines, which is accomplished programmatically by calling the Galaxy API.
Upgrading tripal core to drupal 9 through community development Drupal is frequently updated with new features and improved security, and Tripal responds to leverage these advances. Community-driven development of Tripal 4, which will allow Tripal to run on Drupal 9, is currently underway and includes collaborators from a growing list of organizations. A large collection of resources and training materials has already been created. Code is maintained in a GitHub repository, which features a detailed task list separated into easily approachable issues. Weekly group meetings help organize the work, develop collaborations and strengthen the community. Goals during these meetings include code review, discussions on software design and learning about tools to aid in development. State-of-theart web development tools, such as symfony (https://symfony.
com/), Composer (https://getcomposer. org/) and Twig (https:// twig. symfony. com/), which are already integrated with Drupal 9, are being incorporated into Tripal to help the community leverage these technologies. Developers that contribute to Tripal Core development are not just helping the community; they gain familiarity with the new version that will help with upgrading their existing Tripal extension modules and creating new ones for Tripal 4.
Impact The Tripal platform is used by at least 31 publicly available biological data portals and one in development (Supplementary Figure  1 , see Supplementary Data available online at http://bib. oxfo rdjournal. org/, and Table  1 ). As the software is open source, there are likely other databases leveraging Tripal that are unknown to the broader Tripal community, as evidenced by the Drupal software module system reporting 130 publicly available installations. To quantify the impact of Tripal as well as the experiences and future development priorities of the Tripal community, two community surveys were developed in July of 2020. The first queried each database on details relating to data types stored, Tripal modules utilized, financial support, users served and personnel. The second was an anonymous survey for those utilizing Tripal in their work.