article-specific data

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

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.

RRID:BDSC_50340

RRID:MMRRC_000001-UNC

AB_572208

RRID AB_2565444

AB_2223496

Rattus norvegicus

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.

Figure

2433S

ATCC, # CRL-11268

A11122

A00702

1010-05

711-035-152

F3165

C57BL/6

β-actin

Cat# JAX_000664, RRID: IMSR_JAX:000664),

SCIBOT_SAYS_UNRESOLVED_CURATOR_SAYS_RRID_AND_UNRECOGNIZED

RRID:SCR_003070

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.

___ 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

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

RRID:MGI:5882597

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

October

limit

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.

publishers

surprisingly

their

later reproduce the experiment being analyzed.

​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.  

founding

Secured NIH funding.

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

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

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.

despite using datasets identical to the originals.

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

downloaded as a zip file

knockdown

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)

Related to

SciBot.

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

Abstract A08: Extensive subclonal mutations in human colorectal cancers detected by Duplex Sequencing

Abstract LB-338: Extensive subclonal mutations in human colorectal cancers detected by duplex sequencing

disorders

Peter's anomaly

sc-138763 from Santa Cruz Biotechnology Inc

for example if a cell line is known to be contaminated

RRID: RRID:SCR_006397

Jax:004453; RRID:IMSR_JAX:004453

CD43BD PharMingenClone S7; RRID: AB_10895376

anti-hCD49b-PEBDCat#555669; RRID: AB_396022

BD BiosciencesCat#565564; RRID:AB_2722547

Resource information A simple three-column table allows full reporting of reagent and resource information, including their source and identifiers.

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

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

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

Uniform resolution of compact identifiers for biomedical data.

Uniform resolution of compact identifiers for biomedical data

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

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.

S-2000

The Antibody Registry: Reagent: Antibodies - SciCrunch

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

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.

such as title, abstract or keywords

This list holds 451 cell lines

Eteplirsen for the treatment of Duchenne muscular dystrophy

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.

Spinal cord

cannabinoid

MGC Fully Sequenced Human CEL cDNA

A proposal for validation of antibodies

antibodies: also report source, characteristics, dilutions and how they were validated

Figure 3. Percent correctly reported RRIDs.

Riding on sidewalks should be avoided and may be prohibited in some areas.

Identified Cellular Correlates of Neocortical Ripple and High-Gamma Oscillations during Spindles of Natural Sleep

The Extracellular Matrix Protein Brevican Limits Time-Dependent Enhancement of Cocaine Conditioned Place Preference

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

The following primary antibodies were used and incubated overnight at 4 °C: mouse monoclonal anti-cyclin D1 (1:1000, Neomarker, Fremont, CA, USA)

Expression and purification of the nucleocapsid protein of Schmallenberg virus, and preparation and characterization of a monoclonal antibody against this protein

TNF-alpha neutralizing antibody blocks thermal sensitivity induced by compound 48/80-provoked mast cell degranulation

Fatty acid oxidation in macrophage polarization

RRID: MGI_2178111

Down Syndrome Developmental Brain Transcriptome Reveals Defective Oligodendrocyte Differentiation and Myelination

Peripheral monocytes are functionally altered and invade the CNS in ALS patients

Heterogeneous Optimization Framework: Reproducible Preprocessing of Multi-Spectral Clinical MRI for Neuro-Oncology Imaging Research

Context-Dependent Gait Choice Elicited by EphA4 Mutation in Lbx1 Spinal Interneurons

Experimental febrile seizures impair interastrocytic gap junction coupling in juvenile mice

NMDA Receptor-Dependent LTD Requires Transient Synaptic Incorporation of Ca2+-Permeable AMPARs Mediated by AKAP150-Anchored PKA and Calcineurin

Loss of OMA1 delays neurodegeneration by preventing stress-induced OPA1 processing in mitochondria

Netrin-1LacZ/+ (Ntn1Gt(pGT1.8TM)629Wcs) (referred to as Ntn-1LacZ/+)

α-Axonin-1

α-LH2

α-Sox1

α-Chx10

α-Tag-1

α-Robo3

α-Evx1/2

Mab-Tag-1

Mab-Nkx2.2

Mab-RC2

Mab-Nestin

Chicken α-GFP

α-β-galatosidase

Scalable Brain Atlas

3dBAR

CoCoMac

Tumor necrosis factor-inducible gene 6 protein: A novel neuroprotective factor against inflammation-induced developmental brain injury

Segregated Foxc2, NFATc1 and connexin expression at normal developing venous valves, and connexin-specific differences in the valve phenotypes of Cx37, Cx43, and Cx47 knockout mice

Sharing self-related information is associated with intrinsic functional connectivity of cortical midline brain regions

Psychiatric Risk Gene Transcription Factor 4 Regulates Intrinsic Excitability of Prefrontal Neurons via Repression of SCN10a and KCNQ1

NiftyFit: a Software Package for Multi-parametric Model-Fitting of 4D Magnetic Resonance Imaging Data

Pioneering Activity of the C-Terminal Domain of EBF1 Shapes the Chromatin Landscape for B Cell Programming

Generation of a Xenopus laevis F1 albino J strain by genome editing and oocyte host-transfer

Peripheral injury of pelvic visceral sensory nerves alters GFRα (GDNF family receptor alpha) localization in sensory and autonomic pathways of the sacral spinal cord

s-Adenosylmethionine Levels Govern Innate Immunity through Distinct Methylation-Dependent Pathways

Segregated Glycine-Glutamate Co-transmission from vGluT3 Amacrine Cells to Contrast-Suppressed and Contrast-Enhanced Retinal Circuits

Broadening the spectrum of controls for skin biopsy in painful neuropathies: spondylotic cervical myelopathy patients with painful feet

Sustained release of neurotrophin-3 via calcium phosphate-coated sutures promotes axonal regeneration after spinal cord injury

Individual heritable differences result in unique cell lymphocyte receptor repertoires of naïve and antigen-experienced cells

GABAergic Neuron-Specific Loss of Ube3a Causes Angelman Syndrome-Like EEG Abnormalities and Enhances Seizure Susceptibility

Retinal remodeling in human retinitis pigmentosa

KIF5C S176 Phosphorylation Regulates Microtubule Binding and Transport Efficiency in Mammalian Neurons

Methoxychlor and fenvalerate induce neuronal death by reducing GluR2 expression

Electrochemical detection of protein glycosylation using lectin and protein–gold affinity interactions

A distinct plasmablast and naive B-cell phenotype in primary immune thrombocytopenia

Lymphatic endothelial cells efferent to inflamed joints produce iNOS and inhibit lymphatic vessel contraction and drainage in TNF-induced arthritis in mice

Nanovesicle-targeted Kv1.3 knockdown in memory T cells suppresses CD40L expression and memory phenotype

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

Germline Competent Pluripotent Mouse Stem Cells Generated by Plasmid Vectors

Anti-inflammatory TIPE2 inhibits angiogenic VEGF in retinal pigment epithelium

Boosting Apoptotic Cell Clearance by Colonic Epithelial Cells Attenuates Inflammation In Vivo

Acetylated Tau Obstructs KIBRA-Mediated Signaling in Synaptic Plasticity and Promotes Tauopathy-Related Memory Loss

Optogenetic and chemogenetic insights into the food addiction hypothesis

Sensory innervation of the guinea pig colon and rectum compared using retrograde tracing and immunohistochemistry

GTF2E2 Mutations Destabilize the General Transcription Factor Complex TFIIE in Individuals with DNA Repair-Proficient Trichothiodystrophy

GTF2E2 Mutations Destabilize the General Transcription Factor Complex TFIIE in Individuals with DNA Repair-Proficient Trichothiodystrophy

An Essential Role for SHARPIN in the Regulation of Caspase 1 Activity in Sepsis

Characterization of multiciliated ependymal cells that emerge in the neurogenic niche of the aged zebrafish brain

Characterization of multiciliated ependymal cells that emerge in the neurogenic niche of the aged zebrafish brain

Overexpression of heat shock factor 1 maintains TAR DNA binding protein 43 solubility via induction of inducible heat shock protein 70 in cultured cells

Isolation and Identification of ER Associated Proteins with Unique Expression Changes Specific to the V144D SPTLC1 Mutations in HSN-I