dataesr/scientific-paragraphs-categorization huggingface dataset:
Methods The initial stages of developing the framework for the database consisted of assessing the requirements of those working with image-based data through end user group discussions, both informally and as part of an international workshop. This included the need for both online and offline databases and printable catalogues for use in making identifications at sea. We reviewed current relevant databases and database standards. These were focused around the Darwin Core standard, the Ocean Biogeographic Information System (OBIS), and the World Register of Marine Species databases (WoRMS), which are all used regularly by the end user community. The Darwin Core is an international standard set of terms and definitions that facilitates sharing biodiversity data  [84]. The Darwin Core quick reference guide (http://rs.
tdwg. org/ -A ) comprise a set of text files, including both the dataset (. csv) and a document (. xml) which describes the included files, fields, and their relationships. This offers a standard format used to describe biodiversity data and is being commonly employed to share more complex and structured datasets. OBIS  [87]  was originally developed as the information management component of the Census of Marine Life (2000-2010) programme. OBIS founder, Dr. J. F. Grassle, articulated the vision of OBIS as "an online, worldwide atlas for accessing, modelling and mapping marine biological data in a multidimensional geographic context". The OBIS database currently consists of over 55 million observations of nearly 124,000 marine species. In 2009, OBIS was adopted as a project by the International Oceanographic Data and Information Exchange (IODE) programme of the Intergovernmental Oceanographic Commission (IOC) of UNESCO.
It represents an internationally important archive for species distribution data. OBIS is closely linked with WoRMS, which provides the taxonomic backbone, and geospatial data are provided by the Marine Regions database. Additional functionality includes the taxon match tool for resolving names used by other similar platforms, providing crucial quality control support for taxonomic data among the research community and biodiversity platforms  [89]. WoRMS is an authoritative classification and catalogue of marine names including information on synonymy, and is curated by around 400 taxonomists globally, in accordance with best practice [88,  89, 90]. The content of WoRMS is managed by taxonomic and thematic experts, who are responsible for controlling the quality of the information contained within the database  [89].
WoRMS is underpinned by the Aphia platform, which is a Microsoft Structured Query Language (MS SQL) database, containing over 400 fields spread over more than 80 related tables. This infrastructure is designed to capture taxonomic and related data and information. WoRMS is also the basis of the World Register of Deep-Sea Species (WoRDSS), which, through its app, Deep Sea ID  [68] , represents one of the few existing image-based deepsea species guides (but see Table  1 ). The Marine Regions database  [91]  provides a standard, relational list of geographic names, coupled with information and maps of the geographic location of these features. All geographic objects of the Marine Regions database have a unique ID, called the Marine Regions Geographic Identifier (MRGID). The different geographic objects are determined by a placetype and coordinates.
While the coordinates are represented as different vector data types being a point, a line or a polygon, a placetype provides contextual information to the geographic objects, for example a sea, a bay, a ridge, a sandbank or an undersea trench. Following the initial review of relevant databases and database standards, a strawman database architecture, to facilitate the standardisation of morphospecies reference image catalogues between individuals / groups, was proposed and circulated to an international team of end users, database specialists and programmers. An international workshop funded by the Deep-Sea Biology Society was held at Plymouth University, UK, on the 4 th -5 th December 2017, where the draft structure was reviewed and refined. The workshop consisted of a cross section of attendees including major dataset holders, computer scientists, taxonomists, benthic ecologists, and representatives from WoRMS / WoRDSS.
End product needs Workshop participants, and specifically those engaged in image-based analysis, felt the most critical tools urgently required to support their work were in-situ photo-guides in book format (hard copy or e-book), a standard reference morphospecies taxonomic tree (or annotation scheme) that can be imported into different annotation software, and on-line user-friendly image reference catalogues that include information on characteristics used to classify animals as belonging to a particular OTU. The final database structure must therefore be such that these end-use products can be easily created from the database by a query using purpose-built web-accessible software as part of future developments.
Database structure The final database structure consists of two tables that contain fields that map onto Darwin Core fields, together with additional fields for which no Darwin Core equivalent could be established. Table  2  is the OTU table. It documents the OTU, and primarily maps to fields from the Darwin Core classes "Taxon" and "Identification". Table  3  is the image table. It documents the individual image file and maps onto fields from multiple Darwin Core classes, including "Occurrence", "Identification", "Event", "Location", "Record-level", and "Organism". The two tables are related via the "OTU" field. This structure allows a single OTU (one entry into Table  2 ) to be related to multiple example images of the OTU (many entries in Table  3 ). The OTU table (Table  2 ) consists of a GUID field "Number", the inclusion of which is standard practice in database tables.
The "OTU" field is a unique number given to this taxon and is initially assigned by the user. The subsequent four fields: "scientificName", "scientificNa-meID", "scientificNameAuthorship", "taxonRank", provide the link to the WoRMS database. The link is via the "scientificNameID" field, which requires the user to input the appropriate Life Science Identifier (LSID) for the OTU drawn from the WoRMS database. Each taxon in WoRMS receives a unique and persistent identifier, known as the AphiaID. This AphiaID can be expanded to a LSID. WoRMS has implemented LSIDs for all its taxonomic names and they are displayed on each taxon page. The LSID integrates the AphiaID and so is the preferred option, of the two possible fields, to use as a link. The appropriate LSID for an OTU is the lowest formal taxonomic rank that can be assigned to an image.
For some taxa, this may be at the species level; however, for many image-based identifications it will be at a higher taxonomic level, such as Family, Class or Phylum level. Use of the LSID field ensures that the OTU can be linked to standard taxonomic nomenclature and the related taxonomic hierarchy. Using this LSID, the other three fields within the database ("scientificName", "scientificNameAuthorship", "taxonRank") can be auto-populated from WoRMS. The "Morphospecies" field maps onto the "identificationQualifier" field in Darwin Core and allows the input of extra details distinguishing between different morphotypes; for example, Brisingidae msp1, or in the case of sponges, Porifera encrusting msp1, Porifera branching msp1. Thus, entries into this field will be of the form msp1, msp2, encrusting msp1, branching msp1, etc.
We feel it is important to ensure that the terminology used to define location is consistent with a published standard. In addition, we want to ensure that, in the future, users will be able to construct local morphospecies reference image catalogues based on selection of an area through mapping software. The Marine Regions database  [91]  is ideally placed to provide this geospatial standard. Its use will also ensure compatibility with OBIS such that this database can share data with OBIS and vice versa. The required fields "locality" and "loca-tionID" provide the link to the Marine Regions database. The user must input the appropriate "locality" and "locationID" for the image drawn from the Marine Regions database. The "loca-tionRemarks" field is an optional free text field that allows users to capture more detailed location information that is not captured by the options available in the Marine Regions database.
The fields "minimumDepthInMeters", "maximumDepthInMeters" are also required as species distributions are structured with depth  [92]  and this characteristic is likely to be important in the development of future field guides. The remaining fields, "decimalLatitude", "decimalLongitude", are optional so as to accommodate older data and / or sensitive data, for example, from industry partners. The fields pertaining to the Darwin Core class "Record-level" focus on ownership and origin of the image. Required information includes the name of the institution that owns the image ("institutionID"), a licence document ("dcterms:license"), the name of the person / institution managing right over the image ("dcterms:rightsHolder"), and the terms of access to the image ("dcterms:accessRights"). It is anticipated that a standard licencing arrangement can be agreed to upon submission of material to the database, whereby image ownership is retained by the organisation / individual submitting but use for scientific purposes is freely granted.
Use of images for commercial gain would be prohibited. There are existing licencing models for WoRDSS and these can be replicated here. Optional fields allow the identification ("collectionID") and citation ("bibliographicCitation") of any previously published or inhouse morphospecies reference image catalogues from which the image data have been drawn. The modified field is autopopulated and is the most recent date-time on which the resource was changed. There are just two fields that relate to the image collection event via the Darwin Core class "Event". These are the fields "RawImage", which maps to the Darwin Core "eventID" field, and "habitat". It is not the intention of this database to capture details of the research cruises, ROV dives, etc. , on which the organism images were taken.
These details are not overly important to the creation of a field guide. However, should this information be viewed as important in the future, we suggest that images are given the name of the original image from which the organism was cropped, and that this name be extended to consist of the following elements: CruiseNumber_StationNumber_timestamp_imagename. The "habitat" field is able to capture the geomorphological setting in which the organism was observed, e. g. seamount, canyon, mid-ocean ridge. We felt this information might be useful in the development of a field guide. The ideal situation would be to use standardised terms to describe these settings. We suggest the use of Greene et al. [93]  as a standard reference; however, the European Nature Information System (EUNIS)  [94, 95]  or other classification systems may also provide a reasonable standard and the standard used could be indicated when data are submitted.
As always though, it is preferable to use standard terminology to record substrate and there are many standards available. Among workshop participants, there was no consensus on methods of substrate interpretation from image data, and the terminology standards used. Some use EUNIS  [94, 95] , some a modified Folk  [96]  classification and others percentage of Wentworth  [97]  sediment size classes. The "SubstrateMethod" field allows the user to indicate the standard they have followed. The "Size" field, standardised to centimetres, is self-explanatory and may be useful in the future development of a field guide. The "Project-Name" field offers the opportunity to credit specific projects with provision of imagery, while the "Link to external database" field enables links to be made to source on-line morphospecies reference image catalogues.
A framework for coordination While the database structure outlined above provides the means to archive data, the development of a unified morphospecies reference image catalogue requires a management structure to curate the database and manage new data submissions. The WoRMS database provides a model that can be adapted for use with this database. WoRMS is curated by teams who are responsible for different taxonomic groups. Each team is led by an editor who takes overall responsibility for that group. We suggest that the morphospecies reference image database is similarly managed by teams focused at the taxonomic grouping level. The appropriate taxonomic grouping will vary depending on variety represented by each phylogenetic level of the group, and expertise available. For example, Hexacorallia may have separate teams grouped at the Order level (e.
g. Scleractinia, Actiniaria, Antipatharia), whereas Echinodermata may have separate teams grouped at Class level (e. g. Asteroidea, Echinoidea, etc. ). Each team will consist of experts in taxonomy of the group plus ecologists engaged in field identification of organisms from imagery. We felt it was important to have both taxonomists and field ecologists working together, to ensure that the final database considers both taxonomic rigor and the practical use of the images. Each team will have a nominated lead, and leads will come together, as a steering committee, to ensure that a standard approach to data organisation and curation is achieved across the entire database. We anticipate a two-stage process whereby an initial effort is made to collate and compile existing morphospecies reference image catalogues at a regional level using the new database structure described above as a data transfer format.
In this format not all fields will need to be populated by those submitting data, for example the GUID fields, and other autopopulated fields. This initial effort to compile existing catalogues would be followed by new and on-going submissions of data, including from those encountering new organisms not in the existing database, and from those with higher quality images of organisms already listed in the database (Fig  2 ). We have committed to stage 1 of this process and morphospecies reference image databases held by all authors have been entered into this new database format and submitted to a central repository. Curation teams are now bringing these data submissions together into a single database. Stage 2 of this process will involve the effort of the global community and could potentially be a focus for the up-coming UN Decade of Ocean Science for Sustainable Development  (2021) (2022) (2023) (2024) (2025) (2026) (2027) (2028) (2029) (2030).
This could be a very light-touch involvement, where end users simply submit images of new organisms not currently present in the database to the database for inclusion (Fig  2 ). Or it could be a more targeted and active involvement aimed at raising the quality of the data already in the database. For example, principal investigators of research cruises could actively help to move taxa from "identificationVerificationStatus" 1 to level 3 by targeted insitu imaging and collection of organisms on an opportunistic basis. Raising the quality of the data in the database should be a priority over the next decade, and with that the recognition of the importance of skills in taxonomy and species identification. A concerted effort to ground truth species identified from imagery only, should be made in order to provide robust tools with which to monitor ecosystems.
Immediate advances enabled by the development of a common reference standard We have proposed a common structure for a database from which a morphospecies reference image catalogue can be built. Our initial development is focused on the North Atlantic deepsea benthos as a case study. However, the structure developed is applicable to any marine region or habitat, and may also be used for terrestrial ecosystems. Individuals need only adopt the structure and populate the tables with their own data. The Standardised Marine Taxon Reference Image Database (SMarTaR-ID) will enable different researchers to bring their data together in a common morphospecies reference image catalogue at an appropriate time. Within the North Atlantic deep sea that time is now. The implementation of coherent monitoring programmes to assess biological biodiversity in marine waters are mandatory under the EU Marine Strategy Framework Directive (MSFD 2008/56/EC), and all European nations are required to monitor sites of community importance every six years.
An image catalogue, such as the one herein proposed, will be a powerful instrument to support monitoring efforts, particularly in poorly surveyed regions. We have outlined a framework by which data can be brought together, curated, and new submissions managed going forward, which follows a successful model already applied by WoRMS. We anticipate the introduction of a common reference standard for the deep sea to enhance significantly our understanding of megafaunal biodiversity by enabling multiple researchers to combine existing datasets to address long-standing ecological questions. This is particularly the case for hard substrate habitats that dominate features, such as seamounts, ridges, banks, abyssal hills, canyons, and areas of the continental slope, and for which image-based techniques remain the only effective means of survey.
Past exploration of the deep-sea epibenthic megafauna generated many paradigms, but these were largely built on data obtained using trawls and sledges. Video and still image-based tools have facilitated quantitative sampling of previously inaccessible habitats; and the resulting new findings are challenging the prevailing view of deep-sea ecosystems  [98]. However, these new datasets are often limited to individual features or feature types (e. g. seamounts:  [99, 100] , abyssal hills:  [101]  slopes:  [66, 102, 103]  canyons:  [48, 64, 104, 105, 106] ; ridges:  [107] , fracture zones:  [100] , and hydrothermal vents:  [108] ) and thus limit our ability to generalise findings. In their review of major outstanding questions in deep-sea biogeography  [109]  concluded, among other things, that an integrated biogeographic framework of hard-substrate areas of the deep sea was required to yield more realistic estimates of endemism/cosmopolitanism.
It has been repeatedly argued that concerted efforts to link existing independent data streams together to examine long-standing questions of deep-sea diversity are very much needed in order to move the field forward  [109, 110]. The proposed database will facilitate these advances. We anticipate that this common reference standard will provide an invaluable tool for environmental managers, industry and wider stakeholders. For environmental managers, it will, for example, enable the development of clearer descriptions and definitions of habitats of conservation concern. For example, deep-sea sponge aggregations potentially qualify as Vulnerable Marine Ecosystems (VME) under the United Nations General Assembly (UNGA) Resolution 61/105. They are also classed as a threatened and declining ecosystem under Annex V of the Oslo-Paris (OSPAR) Convention for the Protection of the Marine Environment of the North East Atlantic.
For industry, this could also decrease levels of risk associated with the assessments as well as decreased analysis time and costs for survey data, and would be a particularly powerful tool if industry could include their own data in the database and play an active role in providing images and survey data. The need for a standard approach in industry was recently highlighted by the development of the deep-sea mining industry in the Clarion Clipperton Zone (CCZ) of the central Pacific. Here, baseline data collection is taking place, commonly including seabed imaging-based assessments of megafauna  [29, 47, 65, 112, 113]. Without a consistent morphospecies reference image catalogue it is difficult to compare studies and generate regional syntheses. This greatly hampers conservation and management efforts, which commonly rely on information on biodiversity, species ranges and behaviour-ecological properties that are difficult to assess without good quality and consistent identifications.
Recent work to document megafaunal diversity will help (e. g. 47, 65) , but widely adopted and regularly updated catalogues will be vital for improving scientific understanding and effective environmental management. A common morphospecies reference image catalogue may also serve as a tool to support the identification of taxa from fisheries bycatch by fisheries observers (e. g. [114]. While our proposed database focuses on in-situ images of taxa, we advocate, and have provided for within the proposed database structure, the collection of ex-situ images of taxa. There are a number of existing image guides designed for use by fisheries observers that provide ex-situ images of VME indicator taxa (Table  1 ). This database could supplement existing guides by providing additional imagery. Interestingly, it may also provide a link between in-situ and ex-situ taxon identification, which may ultimately allow fisheries bycatch data to be pooled with in-situ image data, again broadening our understanding of species distributions (e.
Future advances enabled by the development of a common reference standard The development of a common reference standard has the potential to advance significantly the field of offshore and deep-sea marine ecology. The ability to pool datasets across time and space will allow us to address a greater range of questions about the offshore and deep-sea benthic ecosystem than is currently possible. Critically, it will enable us to raise standards of identification from image data through the development of training materials and quality control measures. Efforts to develop such tools for shallow water have been undertaken by the UK's National Marine Biological Association Quality Control scheme (NMBAQC). This programme is steered by a range of academic and governmental organisations, and provides guidance on best practice, as well as identification guides, taxonomic workshops, training exercises and quality control ring tests.
These characteristics are then organised into pathways of character state choices (steps) that lead to identifications. In order to move forward with the development of much-needed field keys to deep-water taxa, we must first develop an appropriate standard reference against which to assess new observations. This reference point remains the holotype specimen. Our proposed database will establish an image 'similitype' (or a series of images that contribute to the similitype) to accompany a physical specimen that has been identified with reference to the holotype of a species, or through matching DNA sequences to other specimens identified with reference to the holotype of a species, and thus link traditional taxonomy to field identification. This approach will provide a much-needed strategy to advance the taxonomic description of species based on multisource information collected by both ecologists and taxonomists  [117, 118].