dataesr/scientific-paragraphs-categorization huggingface dataset:
1988; Stalpers et al. 1990). Unfortunately, the short-term nature of the funding prohibited this initiative from keeping pace with the development of informatics tools and the initiative was thus progressively abandoned. Nevertheless, MINE had a very positive impact on European CCs; indeed, a number of them retain all, or part, of the MINE dataset in their catalogues to this day. MINE was a landmark in CC collaboration on database projects, but CCs were unable to capitalize on this initiative to truly harmonize their data handling and use. Building on experiences such as MINE and the subsequent EU-funded project Common Access to Biological Resources and Information (CABRI, http://www. cabri. org/)  (Romano et al. 2005) , and enriched by the present survey of CC users and curators, this report describes how MIRRI can move towards an optimized Information System to facilitate access to the data from CCs at various levels.
1 "Compilation report on outputs from WP2 tasks 1-5, intermediate findings, conclusions and recommendations" (http://dx. doi. org/10. 5281/zenodo. 49678). Many of the responses were provided confidentially, and in such cases the source data are not included in the public report. User feedback about needs and expectations related to the use of microbial resources and associated services was compiled, analysed, and evaluated, and will serve as the basis for the design and resultant output of MIRRI's Information System. Two users groups, academic and industrial, were identified as having broadly different needs and expectations. Nevertheless, together, they were in agreement about the need to broaden public CC holdings and services to improve access to microbial expertise and data, and for the need to introduce mechanisms to optimize the MIRRI's genetic resources and associated information, counselling and services.
Analysis of the data provision requests from users can be separated into two main categories: (1) availability of improved and reliable metadata, and (2) improved interoperability between databases. These are described below and a more full coverage is given by the project deliverables D8. 4 Report on comparison of various integration software operating in Life Sciences (https://zenodo. org/record/49968) and D8. 6 Report on human and programmatic access and on documentation development and contents annotation (https://zenodo. org/record/49970).
Improved and reliable metadata Taxonomy The use of DNA sequencing has led to numerous taxonomic changes resulting in a large number of species names becoming obsolete and being replaced by newly created ones. However, a large majority of CC users, and specifically those outside the field of taxonomy, do not keep up to date with microbial taxonomy. To best serve the needs of such users, databases should allow for searches using the "old"/obsolete species names in addition to the new ones. Although this practice has been implemented in some Information Systems (e. g. , CABRI, http://www. cabri. org/) and web servers (YeastIP, http:// genome. jouy. inra. fr/yeastip), it is quite uncommon. In addition, the user community needs integrated tools to allow automatic correction of misspellings in taxonomic names to ensure comprehensive and thorough responses to search queries.
There is also a clear need to indicate the various changes in taxonomic nomenclature together with the date of change. Some databases are in the process of implementing such controls, for example, DSMZ (http://www. dsmz. de/), LPSN (http://www. bacterio. net/) and Mycobank (http://www. mycobank. org/). An up-to-date Information System will have to utilize such databases to display the name changes for species already deposited into the CCs.
Search range and detail The need for extensive searches across several databases for multiple characteristics has become the norm and consequently, users of microbial information should be able to execute a wide range of search queries. Improving the quality and diversity of possible searches is a prerequisite for the improvement of services provided by the CC to its user community. One of them concerns the scope of the databases and the metrics on the taxonomic diversity of the CC's holdings; metadata that is needed to facilitate user searches. The search strings can be simple queries based on the type of strains, the name of the authors who described them or simply by, the isolator of the strain, the depositor, the year of description, the location of isolation, the substrate of isolation, etc.
Notably, such simple search queries are rarely implemented in online databases. More complex searches could be used to mine metadata for interesting and novel properties from CC databases that cover temperature growth, ability to assimilate substrates like carbon sources (as found in API ® strips), nitrogen sources, ability to ferment various substrates, or specific growth characteristics (thermophily, psychrophily, alcaliphily, aerobic/anaerobic growth, etc. )  (Vasilenko et al. 2011). Data fields can also cover passport data, such as substrate and source of isolation including ecological niches, host specificity (plants, animals), etc. , as well as more detailed information on specific substrates (oil pollution, vegetative residues, various soils, foodstuff, etc. ). More commonly and now a prerequisite is the retrieval of (related) DNA sequences of preserved strains.
As a corollary, various combinations of the above searches are desirable and, to some extent, needed. For example, taxa and their growth parameters, or recently described taxa with their substrate of isolation. Aside from a few databases, such as the ones at the Centre de Ressources Biologiques de l'Institut Pasteur (CRBIP) at http://catalogue. crbip. pasteur. fr/crbip_catalogue/faces/recherche_catalogue, and the CIRM-Levures at http://genome. jouy. inra. fr/cirm/ bdd/, the on-line metadata of other CCs are not organized in a manner that permits searching through a large number of fields simultaneously. Finally, users are now requiring that the output of searches to be delivered as versatile files or tables that are easy to download for further analysis.
Improved interoperability between databases There is a large offer of microorganisms and related data from a number of individual CCs, but simultaneously searching their databases presents a challenge. There have been successful endeavours in this regard e. g. , CABRI (http://www. cabri. org/) and StrainInfo (http:// www. straininfo. net/). The CABRI network services offer integrated access to 25 catalogues including more than 130,000 microbial resources. This was made possible by the definition and adoption of common datasets and a special data format to index the catalogue contents in a coherent manner via the Sequence Retrieval System (SRS, http://www. cabri. org/guidelines/catalogue/CPdata. html)  (Etzold et al. 1996). Using the "Extended Query Form" of the standard SRS interface allows searching of all catalogues together and moreover to define multiple query conditions, at best one for each data field (Fig.
1 ). The StrainInfo database consists of metadata extracted from CC databases, which was then used to create strain passport data to link the various CC numbers of a given strain to information such as taxonomic name, sequence data, and bibliographic references  (Verslyppe et al. 2014 ). Thus, StrainInfo allows searches for strains belonging to a given species, or searches related to a given strain number, through a large number of databases (64 CCs and BRCs are now referenced in StrainInfo, citing 693,800 culture collection accession numbers of 298,124 strains, as indicated at http://www. straininfo. net/stats) (Dawyndt et al. 2005; Verslyppe et al. 2014 ). Searches may be complex and simultaneously include various requests (Fig. 2 ). User feedback also indicates that the provision of combined lists of microbial cultures, from several source collections, in a consistent format would be appreciated as it would facilitate the selection of the most appropriate cultures for their needs, as demonstrated by the two examples cited above.
Curators' requests In the previous section, we discussed some of the users' primary requests and needs. In addition, the curators of CCs have specific needs. A good database must facilitate the curator's work, whilst at the same time facilitate access to the holdings, and related data, of the CCs to their users. In fact, CC curators would desire harmonization in all areas; harmonization that would include the use of Standard Operating Procedures (SOPs), data structures and software tools. This would pave the way to the construction of an integrated CC knowledge system that would allow searching databases on the basis of properties associated with the preserved microorganism. Some recommendations for a CC database have already been published  (WFCC 2010; Technical_Archi-tecture_Group 2008; GBBRCN 2011).
Proposed solutions for increased interoperability between the existing databases The harmonization of data standards has been previously attempted for CCs and a basic level of organization is provided by the Organization for Economic Co-operation and Development (OECD) in their best practices for BRCs through Minimum Data Sets (OECD 2007). Good models for a prototype of a MIRRI request system are also present in existing global Information Systems such as CABRI, Straininfo. net, the World Data Centre for Microorganisms, MycoBank, etc. It must be emphasized that, in parallel to the improvement of databases in European CCs, resources and effort must also be invested in the computerization of information. Additionally, if data is to be interoperable between CC databases, and beyond, common formats for data processing operations and network-access tools suitable for most of the CCs, are essential to facilitate knowledge generation.
Similarly, shared data standards should be used for all the common types of data in CC databases. This should be accompanied by uniform principles of operation and informative SOPs. The first coordinated guidelines for data management were proposed by CABRI, which included rules for producing electronic catalogues in a common format (http:// www. cabri. org/guidelines/catalogue/CPdata. html). They were adopted by the OECD best practice guidelines for microbial BRCs (OECD 2007) and then further developed by the Global Biological Resource Centre Network (GBRCN) demonstration project (http://www. gbrcn. org/ project/final-report. html). The latter project was in collaboration with the European Consortium of Microbial Resources Centres (EMbaRC), which resulted in project deliverable D. NA1. 1.
2 "Guidelines for optimal formatting/annotation of data related to the biological materials" and included in the revised EMbaRC BRC standard (http://www. embarc. eu/deliverables. html). There are at least three ways to implement interoperability as far as a network of databases is concerned. The first relies on the use of common software tools for information processing by partner CCs. For example, instituting a common license to use dedicated software for all partner CCs. This approach is rigid since it does not always take into account the specific needs of individual collections, and/or their different exigencies in terms of IT skills and budget. A possible alternative is to develop new software, preferably collaboratively, under an open source environment. The latter would most likely fit the needs of the collections much better, but it could be expensive both in terms of time and effort, as well as put Fig.
1  The "Extended Query Form" interface of CABRI. The SRS standard interface allows multiple query conditions to be set combined with boolean operators for each indexed data field. The query form for CABRI bacteria catalogues is shown. A possible response to a query would then return, e. g. , all strains of the genus Phyllobacterium (field Name), isolated from Ardisia crispa (field Isolated_from) in Germany (field Geographic_origin) excessive pressure on IT staff of the network's members. A third, more flexible, alternative, typically adopted in these situations, would consist of defining a proper data interface that allows the interoperability between CC Information Systems and third-party software. It would include a portal designed for the purpose of interrogating CC catalogues through the interfaces of their Information Systems.
Providing support to CCs to set up appropriate interfaces for their Information Systems would thus serve as a cost-effective alternative. Whichever option is chosen to construct the Information System of MIRRI, one has to recognize that CC staff will need to be trained in informatics and data processing. Such training will also require improved communication between microbiologists and IT staff. In particular, there will need to be clear and consistent terminology, which would mean that IT personnel would need to be familiarized with microbiological terminology and of microbiologists with IT terminology. We recognize that CCs that lack sufficient IT personnel and skills will have to be aided in this venture.
Harmonization of field content in database If one needs to search various databases in a network, the search-field content has to be controlled both semantically and syntactically. During the first World Data Centre for Microorganisms (WDCMs) seminar held at Beijing, China, in May 2011, evidence for differences in the description of strain properties in collection data fields were demonstrated. For example, data on one strain of Aspergillus brasiliensis  (Varga et al. 2007)  were extracted from four catalogues with the following related strain numbers: ATCC 9642, CBS 246. 65, DSM 63263 and VKM F-1119. A total of 24 data fields for the given strain from each collection were then paired and compared: only two fields in two collections were syntactically identical, i. e. , aside from the same content, they also had the same format.
There was in fact no significant differences in the reported strain properties in the four catalogues, aside from the syntax in the terms used to describe them. This example shows that a mere problem of field values could potentially render common searches of various databases difficult and incoherent. Hence, the need for harmonization of the type and description of data in a network of databases is evident. According to the Taxonomic Databases Working Group (TDWG) roadmap and the experience of the Global Biodiversity Information Facility (GBIF)  (WFCC 2010; Tech-nical_Architecture_Group 2008) , and BioMedBridges (BioMedBridges WP3: ESFRI BMS Standards Description and Harmonization, http://www. biomedbridges. eu/workpackages/wp3), the crucial components for the interoperability of databases are: "community supported vocabularies"; "ontologies expressing shared semantics of data"; "common exchange protocols", and "persistent identifiers".
"Vocabularies" refers to information data standards with detailed specifications of content in data fields (controlled vocabularies), in a specified vocabulary format. On the basis of these standards, identical information for a given concept can be inserted in all involved documents. In our case, in all catalogues of the CC partners. "Community supported" refers to the actual support in adopting and maintaining the tool, i. e. , the vocabulary, over time. The starting point for the definition of a community-supported vocabulary may be the creation of a list of popular fields and related content in the catalogues of community members. To determine the most used fields, online catalogues of the WDCM/CCINFO collections were compared. In addition, MIRRI partners provided the fields they included in their catalogues.
The subsequent elaboration of a list of those fields commonly used by CCs has paved the way to the establishment of a shared list, and to its adoption by the community. This list may be termed "Recommended Datasets" or "Practical Datasets" (PDS), to avoid confusion with previous CABRI definitions. "Ontologies" allow for the semantics of both textual and factual information to be encoded and expressed, which is however often implicit and therefore unusable by a software tool. An ontology is a well-defined description of all concepts inherent in a given knowledge domain and of the relationships among them. The most informative ontologies include all instances of concepts, i. e. , all values that can be validly associated with a concept. These instances can also be expressed by using vocabularies.
In bioinformatics, ontologies have many applications, the most important being data validation and data integration. With respect to data validation, software can be developed to allow the checking of values assigned to information described in the ontology. A simple example is the automatic validation of species names on the basis of a special ontology for microbial names. This could be straightforward, e. g. , comparing values listed in a catalogue with the list of valid names in a vocabulary. It could also be further articulated, e. g. , when assessing the validity of single components of a scientific name [genus, species, approbation, author(s), year] per se, and in conjunction with the other components of the name. Regarding data integration, the assignment of a given ontological concept to a piece of information, for example in a database, allows semantically correct connections between heterogeneous databases to be established.
One possible example relates to the Gene Ontology (GO; http://geneontology. org/), a widely adopted ontology of gene products. It is possible to "annotate" the description of a strain, i. e. , to add GO terms that best fit its properties, to establish a potential connection with all databases that use GO. The shared adoption and use of ontologies is therefore an essential prerequisite for data validation and integration in modern Information Systems. Although some data, such as dates, do not strictly need an ontological description, it is important that all specific information have one. For strain-associated data, special ontologies including all related concepts and their relationships are required, along with lists of instances (vocabularies) that take into account the variety of CC data for each piece of information.
bioontology. org/ ontologies/MEO?p=classes&conceptid=root). In order to verify if this mal-adoption of existing ontologies in the representation of data in CC catalogues applies to other information, MIRRI partners were asked to provide lists of unique values for each field in their catalogues. These values could then be compared to the content of related domain ontologies. The obvious need for ontologies in database networking suggests that where no ontology is available, an appropriate one should be created. This would need to be a joint effort between microbiologists and IT specialists. To this end, a careful evaluation of existing ontologies in biological, agricultural, and biomedical research is needed. This is especially relevant given that the MIRRI Information System should be made interoperable with many other systems that are not strictly linked to microbiology, but that are nonetheless relevant for microbial resources, such as databases of sequences, proteins, enzymes, and chemical compounds.
3 ). Although the GCM and its efficient search portal is an important accomplishment, a number of its features do not cater for the CC users' needs. The data of each CC needs to be manually transferred to the GCM by the CCs themselves, resulting in a number of out-of-date catalogues. Although advanced, searches are not completely versatile; requests combining more than two fields are not available in the GCM. Nevertheless, the GCM catalogue and its search tools remain the most thorough Information System for microbiological services. This example demonstrates that the key response would be to harmonize the fields in the database network as described above. An overview of the main tasks involved in the construction of the MIRRI-IS with a temporal perspective is given in Fig. 4.
Conclusions A set of basic requirements for a European Information System has been defined after analysing the needs of CC curators and CC users from the information provided by the MIRRI survey, and from discussions at the 2nd WDCM symposium held in Beijing in 2011. As it can be seen from the options and solutions to user needs described here, harmonisation and common tools are required. Data standards and mechanisms for their adoption can be laid down in the MIRRI infrastructure partner charter ensuring conformity and delivery of the envisaged MIRRI Information System. There remain a number of steps to deliver the MIRRI Information System beginning with the evaluation of existing software and tools for its construction. Further work on the scope of the MIRRI Information System will examine interoperability between collections' data and other relevant data sets outside collections.
There is a clear requirement to follow common data management standards, including adopting common ontologies, or vocabularies, if the Information System construction is to be successful. CC staff have developed standards for data management in the EU-FP7 project EMbaRC (European Consortium of Microbial Resource Centres) and in the GBRCN (Global Biological Resource Centre Network). These standards will be assessed in the context of the envisaged MIRRI Information System. MIRRI must provide the data needed to facilitate the use of microbial diversity in research and development. Further evaluation of the available data is needed to help design mechanisms to link data sets and make the data interoperable. We identified the need to work closely with the ESFRI initiative ELIXIR (European Life Science Infrastructure for Biological Information) and other players such as Straininfo.
Net, WDCM and its Global Catalogue of Microorganisms database. In order to link CC data to other systems it is imperative to respect a certain number of standards so as to allow third parties to use these data and include them in their analyses. In order to do so, software systems used by CCs need to be able to easily, and ideally automatically, export or expose data using a number of structured formats, that are usually XML-based, and are independent of the format of the original database where data are maintained. There are many initiatives trying to establish biological data standards, as well as standards that are used by biologists, such as geographic, climatic or ecological data. Reinventing such standards is certainly not a good idea. What MIRRI would instead do, is "isolate" a number of standards that are relevant to the type of data that CCs are likely to use, and ensure that the software used by CCs are able to produce and utilise such.
CCs have generally made their individual catalogues available on line making cross collection searches difficult. Only now are they re-engaging with each other in Europe and moving towards the creation of interoperable databases. This endeavour is greatly facilitated by the creation of the Microbial Resource Research Infrastructure (MIRRI, http://www. mirri. org/), a research infrastructure that is being designed in the context of the European Strategy Forum on Research Infrastructures (ESFRI).
Acknowledgements This work has received funding from the  European Consortium of Microbial Resources Centres (EMbaRC)  project ( EU   Seventh Framework Programme Research Infrastructures  ( INFRA-2008-1. 1. 2. 9 : Biological Resources Centres (BRCs)  for microorganisms (Grant Agreement No. FP7-228310 ) and the preparatory phase of MIRRI supported by the  European Commission  (Grant Agreement No. 312251 ).