Early Estonian Printings Database and the Book Damage Atlas

Th is article provides an overview of the Early Estonian Printings (EEP) database and the Book Damage Atlas created within the framework of the Watermarks and Paper in Early Modern Estonia project and of questions that arose in the course of the project. The aim of the project was to consider publications as a whole and to try to combine descriptions of different parts of books into a tool for researchers that is readily available and easy to use. The compilers of the EEP database have relied on the standard worked out by the International Association of Paper Historians (IPH) in their descriptions of paper and watermarks and have also added free-form descriptions of watermarks to the database. Entries in the database are tied in with databases of the European-wide Bernstein watermarks portal The Memory of Paper. Keywords: paper, watermarks, database, book history, preservatio

IKT ja Eesti koolikultuur

Uurimuse käigus otsiti vastuseid järgmistele küsimustele: 1) Millised on erinevused õpetajate diskursustes (IKT kasutamise eesmärgid ja põhjused, sellest tulenev kasu, sellega seonduvad probleemid ja ohud)? 2) Milline teoreetiline/kontseptuaalne raamistik sobib kõige paremini kaasaegse õpikeskkonna analüüsiks, s.h. IKT mõju hindamiseks? 3) Milline on kooli juhtimise ja õpetajate täienduskoolituse osa IKT-ga seotud uuenduste elluviimisel koolis? 4) Millised on need innovaatilised, Eesti oludes tulemuslikud strateegiad, mis aitavad kaasa IKT-ga seotud uuenduste elluviimisele koolis?http://www.innovatsioonikeskus.ee/sites/default/files/tekstifailid/IKT_ja_Eesti%20koolikultuur_2003.pd

FungalTraits:A user-friendly traits database of fungi and fungus-like stramenopiles

The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies. Over the past decades, rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging. In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels. Combining the information from previous efforts such as FUNGuild and Fun(Fun) together with involvement of expert knowledge, we reannotated 10,210 and 151 fungal and Stramenopila genera, respectively. This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera, designed for rapid functional assignments of environmental studies. In order to assign the trait states to fungal species hypotheses, the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences. On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1% dissimilarity threshold

Third-party Annotations: Linking PlutoF platform and the ELIXIR Contextual Data ClearingHouse for the reporting of source material annotation gaps and inaccuracies

Third-party annotations are a valuable resource to improve the quality of public DNA sequences. For example, sequences in International Nucleotide Sequence Databases Collaboration (INSDC) often lack important features like taxon interactions, species level identification, information associated with habitat, locality, country, coordinates, etc. Therefore, initiatives to mine additional information from publications and link to the public DNA sequences have become common practice (e.g. Tedersoo et al. 2011, Nilsson et al. 2014, Groom et al. 2021). However, third-party annotations have their own specific challenges. For example, annotations can be inaccurate and therefore must be open for permanent data management. Further, every DNA sequence (except sequences from type material) can carry different species names, which must be databased as equal scientific hypotheses. PlutoF platform provides such data management services for third-party annotations.PlutoF is an online data management platform and computing service provider for biology and related disciplines. Registered users can enter and manage a wide range of data, e.g., taxon occurrences, metabarcoding data, taxon classifications, traits, and lab data. It also features an annotation module where third-party annotations (on material source, geolocation and habitat, taxonomic identifications, interacting taxa, etc.) can be added to any collection specimen, living culture or DNA sequence record. The UNITE Community is using these services to annotate and improve the quality of INSDC rDNA Internal Transcribed Spacer (ITS) sequence datasets. The National Center for Biotechnology Information (NCBI) is linking its ITS sequences with their annotations in PlutoF. However, there is still missing an automated solution for linking annotations in PlutoF with any sequence and sample record stored in INSDC databases. One of the ambitions of the BiCIKL Project is to solve this through operating the ELIXIR Contextual Data ClearingHouse (CDCH). CDCH offers a light and simple RESTful Application Programming Interface (API) to enable extension, correction and improvement of publicly available annotations on sample and sequence records available in ELIXIR data resources. It facilitates feeding improved or corrected annotations from databases (such as secondary databases, e.g., PlutoF, which consume and curate data from repositories) back to primary repositories (databases of the three INSDC collaborative partners).In the Biodiversity Community Integrated Knowledge Library (BiCIKL) Project, the University of Tartu Natural History Museum is leading the task of linking the two components—the web interface provided by the PlutoF platform and CDCH APIs—to allow user-friendly and effortless reporting of errors and gaps in sequenced material source annotations. The API and web interface will be promoted to those communities (such as taxonomists, those abstracting from the literature, and those already using the community curated data) with the appropriate knowledge and tools who will be encouraged to report their enhanced annotations back to primary repositories

The Taxon Hypothesis Paradigm - On the Unambiguous Detection and Communication of Taxa

Here, we describe the taxon hypothesis (TH) paradigm, which covers the construction, identification, and communication of taxa as datasets. Defining taxa as datasets of individuals and their traits will make taxon identification and most importantly communication of taxa precise and reproducible. This will allow datasets with standardized and atomized traits to be used digitally in identification pipelines and communicated through persistent identifiers. Such datasets are particularly useful in the context of formally undescribed or even physically undiscovered species if data such as sequences from samples of environmental DNA (eDNA) are available. Implementing the TH paradigm will to some extent remove the impediment to hastily discover and formally describe all extant species in that the TH paradigm allows discovery and communication of new species and other taxa also in the absence of formal descriptions. The TH datasets can be connected to a taxonomic backbone providing access to the vast information associated with the tree of life. In parallel to the description of the TH paradigm, we demonstrate how it is implemented in the UNITE digital taxon communication system. UNITE TH datasets include rich data on individuals and their rDNA ITS sequences. These datasets are equipped with digital object identifiers (DOI) that serve to fix their identity in our communication. All datasets are also connected to a GBIF taxonomic backbone. Researchers processing their eDNA samples using UNITE datasets will, thus, be able to publish their findings as taxon occurrences in the GBIF data portal. UNITE species hypothesis (species level THs) datasets are increasingly utilized in taxon identification pipelines and even formally undescribed species can be identified and communicated by using UNITE. The TH paradigm seeks to achieve unambiguous, unique, and traceable communication of taxa and their properties at any level of the tree of life. It offers a rapid way to discover and communicate undescribed species in identification pipelines and data portals before they are lost to the sixth mass extinction

Correction to: FungalTraits: a user friendly traits database of fungi and fungus-like stramenopiles

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FungalTraits : a user-friendly traits database of fungi and fungus-like stramenopiles

The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies. Over the past decades, rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging. In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels. Combining the information from previous efforts such as FUNGuild and FunFun together with involvement of expert knowledge, we reannotated 10,210 and 151 fungal and Stramenopila genera, respectively. This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera, designed for rapid functional assignments of environmental studies. In order to assign the trait states to fungal species hypotheses, the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences. On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1% dissimilarity threshold.Supplementary Information: Fig. S1. Trait distributions of fungal genera in different fungal phyla.Fig. S2. Trait distributions of Stramenopila genera in different Stramenopila phyla.Fig. S3. Distribution of the ten most common fungal guilds among annotated sequences.Table S1. Traits of genera.Table S2. Traits of sequences.Table S3. Traits of species hypothesis.Table S4. Example dataset for genus-level annotation using the vlookup function in Excel.Table S5. Comparison of workflows and outputs conducted in FunTraits and FUNGuild.Supplementary item 1. List of trait states for genera and sequences.Supplementary item 2. Instructions for annotators of fungal ITS sequences.Estonian Science Foundation, the University of Tartu and the European Regional Development Fund.https://www.springer.com/journal/132252021-11-01hj2021BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog