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This work contains the data used to test and evaluate tools for references extraction from papers in PDF format. This work derives from mythesis on the references extraction and parsing tools, where the selected tools are: Anystyle, Cermine, ExCite, Grobid, Pdfssa4met, Scholarcy andScience Parse. The folder PDF_papers contains the 56 papers in PDF used as input dataset. The names of the file are composed by the abridged form of the research field they belong to plus a numeric value which orders them from 1 to 54. As regards z_notes the numbering restarts from 0. These last two files are particular since they do not containing an explicitly named references section. They represent a further test for the tools. These papers have been selected from the work“An Analysis of Citing and Referencing Habits across All Scholarly Disciplines: Approaches and Trends in Bibliographic Metadata Errors.” The folder output_files contains seven sub-folders, one for each tool selected in the thesis, each containing the parsed references for each file of the input datase. Not all the folders contain 56 files since some tools were not able to return an output for all the input PDF papers. The folder goldStand_parsed contains one folder containing the gold standard files of the input dataset (gold_standard_files) and another folder containing the parsed references converted to TEI XML (parsed_output_files). The conversion has been made with the codes published athttps://doi.org/10.5281/zenodo.6182128.

A preliminary note This protocol illustrates the workflow adopted within a scholarly research that operates within the OpenCitations environment, which is an independent infrastructure organization for open scholarship dedicated to the publication of open bibliographic and citation data by the use of Semantic Web (Linked Data) technologies. COCI is the OpenCitations Index of Crossref open DOI-to-DOI citations. Purpose The primary purpose of this research is to find the publishers responsible for the missing citations in COCI (the OpenCitations Index of Crossref open DOI-to-DOI citations) by sending incorrect metadata to Crossref, the publishers to whom such invalid citations point to, and the number of previously invalid citations which are currently valid. Further, the additional aim of the present research is to provide material for future and deeper research on the same subject matter. In particular, we focus on keeping track of the main trends of evolution on the validity of citational data and on providing data to facilitate publishers' identification. Study design/methodology In order to study the invalid citations, we use an already generated CSV file which is available online, containing - for each citation - the valid citing DOI and the invalid cited DOI. First of all, through a DOI API request we check whether the validity state of the cited DOI has changed, and then we use DOI's prefix for a CROSSREF API request, in order to identify the responsible and referenced publishers. Findings For each individual publisher, we retrieve the number of incorrect given citations metadata sent, and the number of invalid citations received, to which we decided to add the information about the number of addressed and received citations validated with the software we developed, and its list of prefixes. We also extract the total number of invalid citations that have since been corrected. Any further material provided as result of this research, such as the lists of validated and still invalid citations, is meant to incentivize future improvements of the studies on this field. Originality/value The results of this research may point us to publishers who generally send out incorrect citation metadata and, inversely, those who generally receive invalid citations. These findings can first of all raise awareness of the accuracy of certain publishing houses in managing their metadata (or lack thereof). Moreover, finding these trends and showcasing the labor of the corrections may lead to increasingly valid citations if the proper measures are taken. Research limitations/implications Based on the available data for COCI, there may be a slight bias in our sample, causing some publishers to be incorrectly represented. Minimal bibliography on related projects Heibi, I., Peroni, S. & Shotton, D. Software review: COCI, the OpenCitations Index of Crossref open DOI-to-DOI citations.Scientometrics 121, 1213–1228 (2019). https://doi.org/10.1007/s11192-019-03217-6. Silvio Peroni, David Shotton (2020). OpenCitations, an infrastructure organization for open scholarship. Quantitative Science Studies, 1(1): 428-444. https://doi.org/10.1162/qss_a_00023. Peroni, S. (2021). Citations to invalid DOI-identified entities obtained from processing DOI-to-DOI citations to add in COCI (1.0). Zenodo. https://doi.org/10.5281/ZENODO.4625300. Related Diagrams In order to improve readability and reusability of our protocol, we provide here the flow diagram representing the steps of the procedure and an image of a simplified explicative scheme of the related software structure .

Although the use of pesticides has highlighted obvious advantages on agricultural yields, intensive and widespread pesticide use raises serious environmental and health concerns. In particular, organophosphate pesticides represent >40% of the totality used in the field of agriculture, and developing countries face the issue of agricultural poisoning, also due to scarce monitoring programs. In this work, a decentralized, miniaturized, sustainable, and portable paper-based electrochemical biosensor for the quantification of organophosphorus pesticides' level has been realized. The proposed approach highlights the use of a very common paper-based substrate, namely, office paper. Office paper offers several advantages due to its nature: it allows one to print conductive strips for electrochemical connection, loading bio-hybrid nanosized probes (Prussian blue, carbon black, and butyrylcholinesterase), evaluating pesticides and reducing waste disposal compared to plastic-based strips. The portable system has been characterized by a low detection limit of 1.3 ng/mL, and accordingly to total discovered pesticide contents in EU agricultural soils, up to ca. 3 μg/mL, it can offer a valuable tool for fast monitoring. To demonstrate its effectiveness, soil and fruit vegetables have been used to perform in situ quantification. Good recovery percentages between 90 and 110% have been achieved in different matrices, highlighting to be suitable for field measurements, and a good correlation has been obtained in comparison with LC-MS analysis.

Converting unstructured data, i.e. data coded in a format which is not structured in a predefined way, such as PDF, into structured data, i.e. clearly defined types of data organised in a structure, has several advantages. One of the most positive effects of this conversion is that data becomes easier to search, both for humans and for algorithms. Even if there are many tools which have this objective, through a systematic review of the existing literature it is possible to understand whether there is a software whose features allow it to have better performances than the others in order to carry out a specific task in this context. This protocol shows the methodology followed in order to make a systematic review of the literature regarding the software dedicated to the extraction and manipulation of references from papers in PDF file format. Thus, the objective of this research, which is reflected on the flow of the literature review methodology, is to retrieve the most suitable software for the specified purpose, i.e.retrieving and manipulating citations from PDF files.

A preliminary note This protocol illustrates the workflow adopted within a scholarly research that operates within the OpenCitations environment, which is an independent infrastructure organization for open scholarship dedicated to the publication of open bibliographic and citation data by the use of Semantic Web (Linked Data) technologies. COCI is the OpenCitations Index of Crossref open DOI-to-DOI citations. Purpose The purpose of this research is to find the publishers responsible for the missing citations in COCI by sending incorrect metadata to Crossref, the publishers to whom such invalid citations point to and the number of previously invalid citations which are currently valid. The ultimate aim would be of contributing to the resolution of this type of problem in order to insert the citations now valid in COCI, and correct those still invalid always in order to increase the number of open citations available and indexed in the OpenCitations project. Study design/methodology In the beginning, we use an already generated CSV file, containing the valid citing DOIs and the invalid cited DOIs, which is available from Peroni, S. (2021). Citations to invalid DOI-identified entities obtained from processing DOI-to-DOI citations to add in COCI (1.0). Zenodo. https://doi.org/10.5281/ZENODO.4625300. These citations to invalid DOIs have been retrieved while processing Crossref data for adding open citations in COCI, but they have not been added in COCI since they point to a non-resolvable cited document. Two REST API services can be of help: the DOI REST API to check if the invalid cited DOI is now valid; and the Crossref REST API to retrieve the publisher from the prefix of the DOI, both for the cited publications and the citing ones. Findings In addition to collecting the names of the publishers involved in these missing citations, either as the publisher of the citing article or as the publisher of the cited article, which was sufficient to answer our research questions, we have decided to collect additional information that can help us to get a better picture of the situation. As regards the JSON file, we found for each individual publisher 1) the number of incorrect given citations metadata sent, and 2) the number of invalid citations received. On the other hand, as required by the initial research questions, we also extracted the total number of invalid citations that have since been corrected. Originality/value The results of this research may point us to publishers who generally send out incorrect citation metadata and, inversely, those who generally receive invalid citations. These findings can first of all raise awareness of the accuracy of certain publishing houses in managing their metadata (or lack thereof). Moreover, finding these trends and showcasing the labor of the corrections may lead to increasingly valid citations if the proper measures are taken. Research limitations/implications Based on the available data for the COCI, there may be a slight bias in our sample, causing some publishers to be incorrectly represented. Minimal bibliography on related projects Heibi, I., Peroni, S. & Shotton, D. Software review: COCI, the OpenCitations Index of Crossref open DOI-to-DOI citations.Scientometrics 121, 1213–1228 (2019). https://doi.org/10.1007/s11192-019-03217-6. Silvio Peroni, David Shotton (2020). OpenCitations, an infrastructure organization for open scholarship. Quantitative Science Studies, 1(1): 428-444. https://doi.org/10.1162/qss_a_00023. Peroni, S. (2021). Citations to invalid DOI-identified entities obtained from processing DOI-to-DOI citations to add in COCI (1.0). Zenodo. https://doi.org/10.5281/ZENODO.4625300.