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# called items with site.data.odrs
- short-name: SASDB
name: Small Angle Scattering Biological Data Bank
description: "SASBDB is a curated repository of freely accessible
and fully searchable SAS experimental data, which are deposited
together with the relevant experimental conditions, sample details,
instrument characteristic and derived models. The quality of
deposited experimental data and the accuracy of models obtained
from SAS and complementary techniques is assessed by the site
link: https://www.sasbdb.org/
pic: https://www.sasbdb.org/media/sasbdb-logo.png
api: https://www.sasbdb.org/rest-api/docs/
- IRI: http://purl.org/pan-science/PaNET/PaNET01124
name: small angle scattering
- short-name: PED
name: Protein Ensemble Database
link: https://proteinensemble.org/
pic: https://proteinensemble.org/assets/logos/PED_logo_blue.svg
description: "PED is a platform for the intrinsically disordered
proteins (IDP) community where ensembles and their corresponding
primary data can be stored and used as benchmarking datasets to
facilitate the development of new ensemble calculation methods."
api: https://proteinensemble.org/api
- short-name: AlphaFold
name: Protein Structure Database
link: https://www.alphafold.ebi.ac.uk/
description: "AlphaFold, the state-of-the-art AI system developed
by DeepMind, is able to computationally predict protein structures
with unprecedented accuracy and speed. Working in partnership with
EMBL’s European Bioinformatics Institute (EMBL-EBI), we’ve released
over 200 million protein structure predictions by AlphaFold that
are freely and openly available to the global scientific community.
Included are nearly all catalogued proteins known to science – with
the potential to increase humanity’s understanding of biology by
api: https://www.alphafold.ebi.ac.uk/api-docs
- short-name: wwPDB
name: Protein Data Bank
link: https://www.wwpdb.org/
pic: https://cdn.rcsb.org/wwpdb/img/core/wwpdb-logo.png
description: "Since 1971, the Protein Data Bank archive (PDB) has
served as the single repository of information about the 3D
structures of proteins, nucleic acids, and complex assemblies."
link: https://www.ebi.ac.uk/emdb/
pic: https://www.ebi.ac.uk/em_static/images/emdb/EMBD_logo_2017_light_background.png
description: "EMDB (the Electron Microscopy Data Bank) is a public
repository for electron cryo-microscopy maps and tomograms of
macromolecular complexes and subcellular structures. It covers a
variety of techniques, including single-particle analysis, electron
tomography, sub-tomogram averaging, fibre diffraction and electron
api: https://www.ebi.ac.uk/emdb/api/
- IRI: http://purl.org/pan-science/PaNET/PaNET01145
name: electron microscopy
- short-name: BMRB
name: Biological Magnetic Resonance Bank
link: https://bmrb.io/
pic: https://bmrb.io/images/BMRB_logo_text.svg
description: "BMRB makes bio-NMR data FAIR. It collects, annotates,
archives, and disseminates spectral and quantitative data derived
from NMR spectroscopic investigations of biological macromolecules
api: https://github.com/bmrb-io/BMRB-API
- short-name: Human Organ Atlas
name: Human Organ Atlas
link: https://human-organ-atlas.esrf.eu/
description: "The Human Organ Atlas is making Hierarchical
Phase-Contrast Tomography (HiP-CT) 3D scans of entire organs,
with ca. 20 micron voxels, open access."
- short-name: TomoBank
name: X-Ray Tomography Data Bank
link: https://tomobank.readthedocs.io/en/latest/index.html
description: "The X-ray Tomography Data Bank or TomoBank, provides
a repository of experimental and simulated data sets with the aim
to foster collaboration among computational scientists, beamline
scientists and experimentalists, to accelerate the development of
tomographic reconstruction and 3D visualization methods and to
speed up their implementation in the various synchrotron facility
data-license: CC-BY-4.0 with exceptions
technique:
- IRI: http://purl.org/pan-science/PaNET/PaNET01129
- short-name: CSD
name: Cambridge Structural Database
link: https://www.ccdc.cam.ac.uk/solutions/software/csd/
pic: https://www.ccdc.cam.ac.uk/media/logo-63497a0632403.svg
description: "The Cambridge Structural Database, or CSD, has been
curated since 1965 from the published literature, direct deposition,
and sources such as patents and PhD theses.<br>
The world’s largest database of small-molecule organic and
metal-organic crystal structure data, the CSD is managed by the
Cambridge Crystallographic Data Centre (CCDC)."
technique:
- IRI: http://purl.org/pan-science/PaNET/PaNET01082
name: crystallography
access: subscription-based
- short-name: CXIDB
name: Coherent X-ray Imaging Data Bank
link: https://cxidb.org/
pic: https://cxidb.org/images/cxidb_logo_large.png
description: "CXIDB offers scientists from all over the world a
unique opportunity to access data from Coherent X-Ray Imaging (CXI)
experiments. The website also serves as the reference for the CXI
file format, in which most of the experimental data on the database
technique:
- name: coherent x-ray imaging
access: free
- short-name: Perovskite DB
name: The Perovskite Database Project
link: https://www.perovskitedatabase.com/
pic: https://www.perovskitedatabase.com/static/assets/img/Logo_version4_small_1.png
description: >
The Perovskite Database Project aims at making all perovskite device data,
both past and future, available in a form adherent to the FAIR data
principles, i.e. findable, accessible, interoperable, and reusable.
In the initial phase of the project, the project team went through the over
16000 perovskite papers published until the end of February 2020 and
extracted data for every single adequately described perovskite solar cell
we could find. For papers published after that, the database relies on
authors to upload their own data.
The project is based around an open database and open-sourced tools
enabling anyone, without any programming experience, to interactively
explore, search, filter, analyse, and visualise the data. The core of those
tools are a set of interactive graphics. The interactive graphics are
hosted by MaterialsZone. To reach the graphics, you will need to create a
free account by filling out this form. Shortly after filling out the form,
you will receive an invitation by email.
access: free after registering
data-license: CC-BY-4.0
name: RefXAS- an open access database of XAS spectra
In the frame of DAPHNE4NFDI, an X-ray absorption spectroscopy (XAS)
reference database called RefXAS has been set-up where users are provided
with well curated XAS reference spectra along with related metadata fields
and online processing tools for visualizing the data. The developed online
procedure enables users to submit a raw dataset along with its associated
metadata via a dedicated website for inclusion in the database. The unique
feature of quality criteria formulated for the uploaded reference data at
the database make users aware about the usability of the data. These
quality criteria are further employed for automatic quality check of the
uploaded data which is then followed by manual curation at the interface.
Implementation of the database includes an upload of metadata to the
Scientific-Catalogue and an upload of files via object storage, with
automated query capabilities through a web server and visualisation of the
data and files. A prototype of the database with integrated quality control
for uploaded spectra has been created, which can process common data types
for X-ray absorption spectra and has a standardized metadata schema.
technique:
- IRI: http://purl.org/pan-science/PaNET/PaNET01196
name: x-ray absorption spectroscopy
- short-name: MX-RDR
name: Macromolecular Xtallography Raw Data Repository
link: https://mxrdr.icm.edu.pl/
pic: https://mxrdr.icm.edu.pl/javax.faces.resource/vecler/img/logo-mxrdr.svg
description: >
The Macromolecular Xtallography Raw Data Repository (MX- RDR) was developed
as a part of an EU funded project, coordinated by ICM UW, which aimed to
create three open access discipline dedicated raw data repositories.
<p>
The MX-RDR repository, which is accessible via the web portal at
https://mxrdr.icm.edu.pl, was designed to archive and provide access to raw
diffraction data collected for macromolecular crystals. It includes tools
for creating datasets of crystallographic metadata by combining information
extracted directly from diffraction images and obtained from a PDB deposit
and/or user input. Each data set is characterized by rich metadata, both to
facilitate their management and long-term curation, and to allow effective
scientific reuse. The resource can be searched using various criteria and
all data are available for unrestricted access and download.
technique:
- IRI: http://purl.org/pan-science/PaNET/PaNET01164
name: macromolecular crystallography
data-license: CC-BY-4.0 / CC0-1.0 / All rights reserved
access: free
- short-name: International XAFS DB
name: International XAFS Database Portal of the Japanese XAFS Society
link: https://ixdb.jxafs.org/
description: >
This International XAFS DB Portal was created with the aim of making XAFS
data from around the world findable.
technique:
- IRI: http://purl.org/pan-science/PaNET/PaNET01197
name: x-ray absorption fine structure
data-license: delegated-license
access: free