417 Matching Annotations
  1. Apr 2021
    1. article-specific data

      You are right, but this is tricky. For us to release publicly which authors missed an IRB statement would likely be counterproductive to our goals. Of course we have the data, I am pretty sure that I sent it to Nico about a year ago.

      Just to demonstrate that this is tricky, I ran an assessment on this paper. So this paper scored a 5/10 in SciScore (which is better than average, but people will not necessarily know that). This is something that may not sit well with all authors if they knew that that there was an automated score of their paper, especially given that we can't score papers locked behind paywalls only the nice authors that make their papers open access.

      The tool found a field sample permit (looks like a false positive), inclusion/exclusion, randomization, and replication.

      SciScore found no Blinding, Power Analysis, Attrition, or subject demographics (these should not be scored)

      It found your git repos and turned the links blue so these are valid. If found that your OSF data link is broken: https://doi.org/10.17605/OSF

      It also is grading you down on the clinical trial identifier which does not exist (I know that this is an example, but sciscore does not know that) NCT12345678

      It also thinks that you guys should have included the RRIDs for ggplot2. I don't know how you feel about software citation principles and whether RRIDs are valid, the tool will take off a couple of points if it thinks that you should have an RRID and you don't.

    2. However, this tool does not include indicators of transparency (e.g., data or code sharing)

      Yes but it does now, check out the new version of the code. Nico's tool looks for different things than we do in terms of data sharing. We look for reuse by "finding" accession numbers of ~25 databases. Nico's tool looks for data that has been shared by authors. It is an important distinction, but not one that you guys go into.

  2. Jan 2021
    1. Nice epic poem Juan Pablo Alperin! Please create a book for my children!

  3. Nov 2020
    1. Resource Identification Initiative To improve the reproducibility of scientific research, the Resource Identification Initiative, aims to provide unique persistent identifiers for key biological resources, including antibodies, cell lines, model organisms and tools. We encourage authors to include unique identifiers - RRIDs- provided by the Resource Identification Portal in the dedicated section of the manuscript. To help authors quickly find the correct identifiers for their materials, there is a single web site where all resource types can be found and a ‘cite this’ button next to each resource, that contains a proper citation text that should be included in the methods section of the manuscript.

      check it out

  4. Sep 2020
  5. Jul 2020
  6. Jun 2020
    1. In stark contrast, the Proceedings of the National Academy of Sciences of the United States of America (PNAS), which put out several reports advocating for the need for increased rigor,22 showed no change in composite score: 3.33 in 2015 to 3.42 in 2019.

      PNAS

    2. Figure

      nature

  7. Apr 2020
    1. 2433S

      suggested: (Cell Signaling Technology Cat# 2433, RRID:AB_2243887)

    2. ATCC, # CRL-11268

      suggested: ATCC Cat# CRL-11268, RRID:CVCL_1926

    3. A11122

      suggested: (Molecular Probes Cat# A-11122, RRID:AB_221569)

    4. A00702

      suggested: (GenScript Cat# A00702, RRID:AB_914102)

    5. 1010-05

      suggested: (SouthernBiotech Cat# 1010-05, RRID:AB_2728714)

    6. 711-035-152

      suggested: (Jackson ImmunoResearch Labs Cat# 711-035-152, RRID:AB_10015282)

    7. F3165

      suggested: (Sigma-Aldrich Cat# F3165, RRID:AB_259529)

    8. C57BL/6

      This is underspecified, J or N strain? they have different RRIDs.

    9. β-actin

      Suggestion: (Thermo Fisher Scientific Cat# R960-25, RRID:AB_2556564)

  8. Mar 2020
    1. SciScore: 6

      This automated review was done on 3/19/2020

      It shows that IRB / Consent statements are present in the paper, but the study did not use blinding or randomization. The study should be considered preliminary.

      See report: https://drive.google.com/file/d/1J6i0mFsAmhUPEb5JLR981CbfzdqgWZjr/view?usp=sharing

    1. SCIBOT_SAYS_UNRESOLVED_CURATOR_SAYS_RRID_AND_UNRECOGNIZED

      missing option SCIBOT_SAYS_UNRESOLVED_CURATOR_SAYS_RRID

  9. Feb 2020
    1. For this study, we downloaded and processed all open access literature available through PubMed Central (PMC, RRID:SCR_004166) in September of 2019. In total, we obtained data from 1,578,964 articles from 4,686 unique journals.

      unfortunately we don't define all with a number.

  10. Oct 2019
    1. ___ Examples of references. Note that when citing RRIDs, the URL must follow the citation format as shown below: Journal Citation: Binoux M, Hossenlopp P. Insulin-like growth factor (IGF) and IGF-binding proteins: comparison of human serum and lymph. J Clin Endocrinol Metab. 1988;67(3):509–514. Abstract Citation: MacLaughlin DT, Cigarros F, Donahoe PK. Mechanism of action of Mullerian inhibiting substance. Program of the 70th Annual Meeting of the Endocrine Society, New Orleans, LA, 1988, p 19 (Abstract P1-21). Book Citation: Bonneville F, Cattin F, Dietemann J-L. Computed tomography of the pituitary gland. Heidelberg: Springer-Verlag; 1986; 15–16. Book Chapter Citation: Burrow GN The Thyroid: nodules and neoplasia. In: Felig P, Baxter JD, Broadus AE, Frohman LA, eds. Endocrinology and metabolism. 2nd ed. New York: McGraw-Hill; 1987:473–507. Repository Citation: Brown C, Jones M, Cohen M. Data from: Medical device-regulation process: review of safety notices and alerts. Dryad Digital Repository 2017. Deposited 2 January 2018. http://doi.org/10.9561/dryad.585t4 Antibody Citation: RRID:AB_2629219 Cell Line Citation: RRID:CVCL_1H60 Organism Citation: RRID:MMRRC_048263-UCD Plasmid Citation: RRID:ADDGENE_104005 Tool Citation: RRID:SCR_007358

      here

    1. recommended name (most frequently, the name provided in the referenced publication) and a list of synonyms;

      ...and yet when the authors of a paper register for an RRID, which they put into the paper you are linking to, you ignore that fact and give the antibody your own identifier without cross linking ...? Here is where I am looking: https://web.expasy.org/abcd/ABCD_AG351 You list this paper as the place where the author describes the antibody: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5182123/ In the paper, the author describes the antibody as: "Monoclonal antibodies (mouse immunoglobulin-γ (IgG)) that bind to GluN1 ATD (RRID: AB_2629508) from Xenopus laevis and Rattus norvegicus were made by immunizing mice with the purified intact GluN1a-GluN2B NMDA receptor (Tajima et al., 2016)." Please note, the author obtained an RRID from the antibodyregistry.org prior to publication of the manuscript, it is nice that you linked the reagents to Uniprot, but I find it disturbing that you ignore the work put in by authors and journal editors to uniquely identify these reagents.

    1. RRID:MGI:5882597

      Please note, this is not an RRID, it marks the allele; to see the appropriate record for please go to http://www.informatics.jax.org/allele/MGI:5882597

  11. Sep 2019
    1. Early-career researchers do not need to wait passively for coveted improvements. We can create communities and push for bottom-up change.

      This is a really important call to action.

    1. October

      december

    2. limit

      reduce?

    3. Because SciScore is completely automated, it is able to operate with far more consistency and speed than peer reviewers, while still picking up even the most minute details.

      Because SciScore is automated, it is a scalable solution, independent of peer reviewers. SciScore gives journals a metric on quality and a means to enforce basic rigor criteria.

    4. publishers

      for peer review

    5. surprisingly

      remove

    6. their

      remove

    7. later reproduce the experiment being analyzed.

      find the tool

    8. ​SciCrunch Inc. was founded in October of 2015 by Drs. Bandrowski and Martone. They have been focused on reproducibility-based issues in the contemporary sciences over the last 15+ years and have developed and lead hundreds of people across dozens of projects during that time including Force11 and the Resource Identification Initiative, which gave rise to the RRID standard now used throughout thousands of journals.  

      odd phrasing; may want to crib some of this from the grant text

    9. founding

      odd

    10. Secured NIH funding.
    11. As a result, this limits the time spent on each research paper, increasing a publisher’s efficiency and the overall reproducibility of research published.

      shorten or remove

    12. submitted to publishers, and increasing reproducibility due to better methods reporting.

      check grammar phrasing seems odd

    13. Peer reviewers are doing a subpar job in enforcing best practices as they focus their attention more on the science and less on the small yet surprisingly important details of the methods.

      peer reviewers are not good at enforcing standards and best practices for the journal. They focus on ... someone or something needs to assess the things they miss

  12. Aug 2019
    1. despite using datasets identical to the originals.

      This is misleading. The paper from Amgen was not a computational replication, so datasets is not the right word, they tried to reproduce the biology and couldn't. This gives the place where wet lab reagents are discussed: https://hyp.is/O9mjSskWEemOE_NFRtyf8A/www.nature.com/articles/483531a Models are also discussed and that can be an ambiguous word, in biology a model is very frequently able to escape the cage or the lab. It is seldom computational. The statement can be valid of computational models as well, but I suspect that the problems in reproducibility have a different flavor.

    1. an attempt was made to contact the original authors, discuss the discrepant findings, exchange reagents and repeat experiments under the authors' direction, occasionally even in the laboratory of the original investigator

      *

  13. Jul 2019
    1. For SciScore, we used standard measures for classification performance: precision P, recall R, and harmonic mean of precision and recall F1. These are defined by the following formulas: the number (#) of correctly recognized labels refers to the number of words that are recognized as cell lines, which were also a cell line according to the curators. The number (#) of true good labels refers to the total number of cell lines according to the curators. P, R, and F1 are calculated on each 10% test set. P= (# of correctly recognized good labels) / (# of recognized good labels) R= (# of correctly recognized good labels) / (# of true good labels) F1=(2*P*R) / (P+R)

      this part explains the standard formula for this.

  14. May 2019
    1. SciBot.

      SciBot lives here: https://github.com/SciCrunch/scibot

      Featured in this remarkably eLife paper (repo was copied to eLife as part of the process of publishing): https://elifesciences.org/articles/41676

  15. Apr 2019
    1. while the Resource Identification Initiative portal [13] contains mainly technologies from PubMed that were manually annotated by curators.

      This is not exactly true, PubMed does not talk about tools because it is an abstract service, tools are discussed in the methods section; furthermore, the initiative uses a hybrid human/machine approach by using the Hypothesis client and a nice custom reader, called scibot. https://github.com/SciCrunch/scibot This enables automated mining and human verification of RRIDs, 180K of them ...and counting.<br> Here is the data we have mined for this one antibody, https://scicrunch.org/resolver/RRID:AB_90755

  16. Mar 2019
    1. sc-138763 from Santa Cruz Biotechnology Inc

      " A troubling finding of our study is that the rabbit polyclonal antibody SC-138763, which clearly does not recognize C9ORF72 in any application, has been used in 15 published manuscripts to ascribe specific properties to the protein in normal and disease states (Table 1). " https://doi.org/10.1101/499350

  17. Jan 2019
  18. Nov 2018
  19. Aug 2018
  20. Jul 2018
  21. Jun 2018
    1. Resource information A simple three-column table allows full reporting of reagent and resource information, including their source and identifiers.

      Here is the table, with RRIDs

  22. May 2018
    1. Mouse Phenome Database: an integrative database and analysis suite for curated empirical phenotype data from laboratory mice.

      Drs. Chessler and Bogue discuss the Mouse Phenome Database in this webinar, recorded on Apr 27, 2018 https://youtu.be/T-_yo1H0CIo?t=1s

    1. Mouse Phenotype Database Integration Consortium: integration [corrected] of mouse phenome data resources.

      Drs. Chessler and Bogue discuss the Mouse Phenome Database in this webinar, recorded on Apr 27, 2018 https://youtu.be/T-_yo1H0CIo?t=1s

    1. Mouse Phenome Database: an integrative database and analysis suite for curated empirical phenotype data from laboratory mice

      Drs. Chessler and Bogue discuss the Mouse Phenome Database in this webinar, recorded on Apr 27, 2018 https://youtu.be/T-_yo1H0CIo?t=1s

    1. Uniform resolution of compact identifiers for biomedical data.

      You could read all this, or you could just watch the movie. Dr. Wimalaratne discusses compact identifiers as part of the Neuro-Tools webinar series, on April 20, 2018

      https://youtu.be/YauhbzNusAk?t=1m38s

    1. Uniform resolution of compact identifiers for biomedical data

      You could read all this, or you could just watch the movie. Dr. Wimalaratne discusses compact identifiers as part of the Neuro-Tools webinar series, on April 20, 2018

      https://youtu.be/YauhbzNusAk?t=1m38s

  23. Mar 2018
    1. Neuroscience Information Framework (NIF) Encyclopedia of Computational Neuroscience 2015 | other DOI: 10.1007/978-1-4614-6675-8_459

      here it is

  24. Feb 2018
    1. However, Simson (2016) has pointed out that the relabeling of antibodies for commercial sale results in the same antibody being available from multiple sources, negating or diminishing the value of the RRID.

      While Mike Simson's blog on Linked in is very well reasoned, it is completely unfair that these authors dismiss our multi, year, multi-journal effort to improve scientific rigor in the literature by using a blog written by the CEO of a company that is showcasing their competitive advantage in the marketplace. If you are a scientist and going to talk yourself into inaction, because there remain imperfections in a multi billion dollar industry, then at least have the research prowess to use peer reviewed literature to do that. Citing a corporate blog here is a copout, as is this argument.

  25. Nov 2017
    1. S-2000

      I think that this is actually from Vector Labs; the RRID for that would be RRID:AB_2336617

  26. Oct 2017
    1. The Antibody Registry: Reagent: Antibodies - SciCrunch

      Please open the LinkOut section then this note will be linked; We are not allowed by PubMed to provide individual links to antibodies, but we have them on our website.

    1. The AntibodyRegistry Database SciCrunch 2009 | other RRID: RRID:SCR_006397 http://identifiers.org/rrid/RRID%3ASCR_006397 URL: http://antibodyregistry.org http://antibodyregistry.org Source: AE Bandrowski Preferred source

      This is not a paper, but an unpublished database; it is part of my ORCID record.

    1. Research Resource Identifiers. The FASEB Journal encourages the use of Research Resource Identifiers (RRIDs), which have been developed in support of NIH's guidelines for rigor and transparency in biomedical publications. RRIDs may be included with other, required, information in the Materials and Methods section, but may not be used as a substitute. Readers without access to RRID information must have enough information to replicate experiments. For more information about RRIDs, visit https://scicrunch.org/resources.

      FASEB now asking for RRIDs

    1. such as title, abstract or keywords

      Again this means that this search is basically missing most of the articles. They are not looking at any papers that do not specifically cite one of the papers that established the cell line, so anything that cites a paper that cited the main one is missing.

    2. This list holds 451 cell lines

      This was only true when the list came out, this is now over 700 cell lines which will likely increase these estimates substantially! I wish they would given the accessed date for this number!

    1. http://retractionwatch.com/2017/10/02/ori-finds-misconduct-case-biologist-paid-100k-university-leave/

      "In the ORI report, published Sept. 29, 2017, the agency determined that El-Remessy had “intentionally, knowingly, or recklessly used the same Western blot bands to represent different experimental results” in three papers — a 2005 paper in Journal of Cell Science, a 2013 paper in PLOS ONE, and a 2007 paper in The FASEB Journal. The Journal Cell Science and The FASEB Journal papers have been retracted. The PLOS ONE paper, which has been cited nine times, according to Clarivate Analytics’ Web of Science, has not yet been corrected or retracted."

    1. http://retractionwatch.com/2017/10/02/ori-finds-misconduct-case-biologist-paid-100k-university-leave/

      "In the ORI report, published Sept. 29, 2017, the agency determined that El-Remessy had “intentionally, knowingly, or recklessly used the same Western blot bands to represent different experimental results” in three papers — a 2005 paper in Journal of Cell Science, a 2013 paper in PLOS ONE, and a 2007 paper in The FASEB Journal. The Journal Cell Science and The FASEB Journal papers have been retracted. The PLOS ONE paper, which has been cited nine times, according to Clarivate Analytics’ Web of Science, has not yet been corrected or retracted."

    1. http://retractionwatch.com/2017/10/02/ori-finds-misconduct-case-biologist-paid-100k-university-leave/

      http://retractionwatch.com/2017/10/02/ori-finds-misconduct-case-biologist-paid-100k-university-leave/

      "In the ORI report, published Sept. 29, 2017, the agency determined that El-Remessy had “intentionally, knowingly, or recklessly used the same Western blot bands to represent different experimental results” in three papers — a 2005 paper in Journal of Cell Science, a 2013 paper in PLOS ONE, and a 2007 paper in The FASEB Journal. The Journal Cell Science and The FASEB Journal papers have been retracted. The PLOS ONE paper, which has been cited nine times, according to Clarivate Analytics’ Web of Science, has not yet been corrected or retracted."

  27. Aug 2017
    1. Scientific rigor: reproducibilityOn April 5, 2017, we added new guidelines for statistical reporting to the JNeurosci Instructions for Authors. While our reviewers have always commented on aspects of experimental design and statistical analyses when evaluating a manuscript, we wanted to create guidelines that would be relevant across the neuroscience field and support effective evaluation by reviewers that was consistent in its rigorous standards for future replication. To create these guidelines, we convened a group of editors with expertise in different subdisciplines. The updated guidelines derived from these discussions focus on including more details of experimental design and making sure that this information is contained within a single section of the Materials and Methods section, entitled Experimental design and statistical analysis, where it can be found more easily.Consistent with these efforts to improve rigor and reproducibility, JNeurosci also encourages authors to include RRIDs for critical reagents used in their studies, including antisera, mouse lines, cell lines, etc.

      Here Dr. Picciotto discusses aligning the Journal of Neuroscience with the NIH guidelines for Rigor and Transparency.

  28. May 2017
    1. MGC Fully Sequenced Human CEL cDNA

      Warning, this reagent is not what it appears to be! Please see Xia et al, JBC 2017: doi:10.1074/jbc.A116.734384 "We recently learned that the cDNA encoding CEL purchased from OpenBiosystems (clone ID 5187959; GenBankTM accession no. BC042510.1) for this work contains a three-base pair in-frame deletion resulting in p.E365del. (The correct sequence should be 356NKGNKKVTEEDFYKLVSEFTITKGL380 and not 356NKGNKKVTE-DFYKLVSEFTITKGL380.) p.E365 is conserved in most primates. The residue is located in a surface loop of the CEL globular domain distant from the catalytic site and the bile acid-binding site."

  29. Apr 2017
    1. A proposal for validation of antibodies

      This paper is the basis of an example Authentication of Key Biological Resources document that we and the UCSD library has put together. Please find it here: http://doi.org/10.6075/J0RB72JC

  30. Feb 2017
    1. Figure 3. Percent correctly reported RRIDs.

      shows accuracy of RRID to be 97% content, 70% syntax

  31. Dec 2016
    1. Riding on sidewalks should be avoided and may be prohibited in some areas.

      HA! Seriously, you need to ride on sidewalks at night if you want to live. Protected, Class I, bike lanes are fine otherwise I am on the sidewalk!

  32. Nov 2016
    1. Hypoxia stimulates proliferation of rat neural stem cells with influence on the expression of cyclin D1 and c-Jun N-terminal protein kinase signaling pathway in vitro
    2. The following primary antibodies were used and incubated overnight at 4 °C: mouse monoclonal anti-cyclin D1 (1:1000, Neomarker, Fremont, CA, USA)

      Neomarker check to see if this is a company bought by Thermo?

    1. Physiological function and inflamed-brain migration of mouse monocyte-derived macrophages following cellular uptake of superparamagnetic iron oxide nanoparticles—Implication of macrophage-based drug delivery into the central nervous system
    1. GTF2E2 Mutations Destabilize the General Transcription Factor Complex TFIIE in Individuals with DNA Repair-Proficient Trichothiodystrophy
    2. GTF2E2 Mutations Destabilize the General Transcription Factor Complex TFIIE in Individuals with DNA Repair-Proficient Trichothiodystrophy
    1. Characterization of multiciliated ependymal cells that emerge in the neurogenic niche of the aged zebrafish brain
    2. Characterization of multiciliated ependymal cells that emerge in the neurogenic niche of the aged zebrafish brain