14 Matching Annotations
  1. Jun 2018
    1. Figure 9. Constraint plots

      This is another example of a form of online data we support for our authors. In this case the 83 objects analyzed in this paper each had graphical representations of the model fits. All 83 elements can be viewed in the online journal via a filmstrip UI element. Readers can read individual captions for each element, download individual plots, or the entire set.

    2. Only a portion of this table is shown here to demonstrate its form and content. A machine-readable version of the full table is available.

      This is an example of one of the Journal's machine readable tables. The reader clicks from the a shortened "example" version of the table inline to the main article to an ASCII text file that they can download and reuse. One of the Journal's data editors built this full ASCII text file from data provided by the author. This process includes standardizing formats, units and column explanations, which are all proofed by the author after the paper has been accepted.

    3. Our posterior samples are available online (10.5281/zenodo.162965).

      This is an example of our current data linking markup. Data links are inline to the text through a parenthetical anchored link to the DOI resource.

      There is a bug in the current version of the article. Our formal practice is to include this in the "Article Data" tab, which didn't happen this time. We will have to do some more work standardizing our production practices. We are also still thinking about how best to markup the anchored text.

      We have not yet adopted a formal XML schema for including data links. We are working on this, which may be made easier when we adopt the most recent JATS schema.

    1. Acero F., Ackermann M., Ajello M. et al (Fermi-LAT) 2015 arXiv:1501.02003Preprint

      Starting in 2014-2015, AAS/IOP started linking to preprints in reference lists if they were the version cited by the author and an accepted manuscript did not at that time exist.

      Thus we now have built in "categories" for references, which could be expanded to include data/software sections.

    2. The most up-to-date version of the open-source package NPTFit may be found at https://github.com/bsafdi/NPTFit and the latest documentation at http://nptfit.readthedocs.io. In addition, the version used in this paper has been archived at https://zenodo.org/record/380469#.WN_pSFPyvMV.

      This is an example of incorrect software citation per the AAS Journal's policy. The Zenodo metadata should have been added to the reference list as a 1st class citation.

      It is also an example of an incorrectly typeset URL. URLs that come from DOIs should be typeset using the DOI string not the resolved URL. It should have read, "version used in this paper has been archived at https://doi.org/10.5281/zenodo.380469"

    3. Foreman-Mackey D., Vousden W., Price-Whelan A. et al 2016 corner.py: corner.py v2.0.0, doi:10.5281/zenodo.53155

      corner.py is one of the more interesting examples of software citations. there are at least 3 different formal references in the wild:

      https://doi.org/10.5281/zenodo.11020 https://doi.org/10.5281/zenodo.53155 https://doi.org/10.21105/joss.00024

      with different versions and author lists.

    1. Barbary K. 2014 sncosmo Zenodo, 10.5281/zenodo.11938

      This software citation losts its version information. We will have to work on our typsetting and production rules, as well as develop formal JATS/NLM XML schema to contain versioning information.

    2. https://doi.org/10.5281/zenodo.11938

      This DOI software archive is also in the Reference list per our Journal's software policy.

    3. The catalog of fakes used to generate the efficiency grids in Section 3 are available in a persistent directory: doi:10.5258/SOTON/D0030.

      This is the dataset related to this article. It contains reproducibility and reusable data for readers.

      Our "article data" tab is suppose to show this entry, but the article data tab is currently linked to the wrong DOI (the Zenodo one highlighted below).

      We do not yet submit this type of data citation as CrossRef metadata. We are still discussing how data citations should appear and be acknowledged in the text.

    4. Software: hotpants, PostgreSQL, realbogus (Bloom et al. 2012) scamp (Bertin 2006), sextractor (Bertin & Arnouts 1996), sncosmo (Barbary 2014), swarp (Bertin et al. 2002), matplotlib (Hunter 2007), numpy (Van Der Walt et al. 2011).

      The AASJournals now highlight software using a paragraph trailing the acknowledgements that lists all software used in the paper's analysis. The software doesn't need to be mentioned in the main text; context-free mentions can be placed here.

      The format is a 2 item tuple containing the short/common name of the software, and a citation or URL for the software.

      In principle this section could be data mined. At the moment it is just a free paragraph in the XML, but could be given more explicit markup to aide in data mining reuse and indexing.

    1. 1- 13 A13 --- Planet Planet 15- 15 I1 --- robust Robust flag (1) 17- 23 F7.3 d Per Orbital period 25- 28 F4.1 Rgeo Rad Planet radius 30- 33 F4.2 Rgeo E_Rad 1{sigma} upper error bound on Rad 35- 38 F4.2 Rgeo e_Rad 1{sigma} lower error bound on Rad 40- 40 A1 --- r_Rad Source of planet-star radius ratio (2) 42- 44 F3.1 solMass Mstar Mass of host star 46- 49 F4.2 solMass E_Mstar 1{sigma} upper error bound on Mstar 51- 54 F4.2 solMass e_Mstar 1{sigma} lower error bound on Mstar 56- 56 I1 --- l_Md Md upper limit flag (3) 58- 63 F6.2 Mgeo Md Planet mass from default prior 65- 69 F5.2 Mgeo E_Md ?="" 1{sigma} upper error bound on Md 71- 74 F4.2 Mgeo e_Md ?="" 1{sigma} lower error bound on Md 76- 81 F6.2 g/cm3 rhod Planet density from default prior 83- 87 F5.2 g/cm3 E_rhod ?="" 1{sigma} upper error bound on rhod 89- 92 F4.2 g/cm3 e_rhod ?="" 1{sigma} lower error bound on rhod 94- 94 I1 --- l_Mh Mh upper limit flag (3) 96-100 F5.1 Mgeo Mh Planet mass from high mass prior 102-107 F6.2 Mgeo E_Mh ?="" 1{sigma} upper error bound on Md 109-112 F4.2 Mgeo e_Mh ?="" 1{sigma} lower error bound on Md 114-119 F6.2 g/cm3 rhoh Planet density from high mass prior 121-126 F6.2 g/cm3 E_rhoh ?="" 1{sigma} upper error bound on rhod 128-131 F4.2 g/cm3 e_rhoh ?="" 1{sigma} lower error bound on rhod 133-155 A23 --- Ref References (4)

      This is the main header block of the AAS Journal's "Machine Readable Format" for structured tables. It is based on the CDS table format, and follows their structuring rules. There are columns for the numerical format, units, labels, and explanations for each column.

    1. Software: Juypter notebook (http://jupyter.org), Jupyterlab (https://github.com/jupyterlab), VOspace (http://www.canfar.net/en/docs/storage), vos (https://pypi.python.org/pypi/vos), VirtualBox (https://www.virtualbox.org), JupyterHub      (https://jupyterhub.readthedocs.io/en/latest/), ipywidgets (https://ipywidgets.readthedocs.io), NuPyCEE (http://nugrid.github.io/NuPyCEE), NuGridSetExplorer (https://github.com/NuGrid/WENDI), hdf5 (https://www.hdfgroup.org), Cyberlaboratories cyberhubs (https://github.com/cyberlaboratories/cyberhubs), Cyberlaboratories astrohubs        (https://github.com/cyberlaboratories/astrohubs), Cyberhubs Docker repository (https://hub.docker.com/u/cyberhubs), Docker (https://www.docker.com), NOAO data lab (http://datalab.noao.edu), ansible (https://www.ansible.com), puppet (https://puppet.com), mesa_h5 (https://github.com/NuGrid/mesa_h5), Python (https://www.python.org), MESA (http://mesa.sourceforge.net), WENDI (http://wendi.nugridstars.org), OpenMP (http://www.openmp.org), MESA-SDK (http://www.astro.wisc.edu/~townsend/static.php?ref=mesasdk), MPI (https://www.open-mpi.org), gfortran (https://gcc.gnu.org/fortran), SuperLU (http://crd-legacy.lbl.gov/~xiaoye/SuperLU), OpenBLAS (http://www.openblas.net), mencoder (http://www.mplayerhq.hu).

      It would be better to see some of these going to bibliographic references instead of URLs though many of them do not list preferred citations.