36 Matching Annotations
  1. Aug 2018
    1. such as DOIs, which might be assigned by, for example, “crossref” or “figshare”

      I have to say publicly that this sentence makes absolutely no sense as crossref and figshare are not comparable assigning authorities. CrossRef is a registration agency of the International DOI Foundation; FigShare is not. Based upon the example given, the assigning-authority for a DOI would only ever be the set of agencies that assign DOIs. FigShare is not one of those agencies. See it is not on the list: https://www.doi.org/registration_agencies.html

  2. 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.

  3. Feb 2018
    1. Let’s use some common units as examples: gram (g), erg (erg), and solar mass per cubic megaparsec (Msun / Mpc33^3). g is an atomic, CGS base unit, erg is an atomic unit in CGS, but is not a base unit, and Msun/Mpc33^3 is a combination of atomic units, which are not in CGS, and one of them even has an SI prefix. The dimensions of g are mass and the cgs factor is 1. The dimensions of erg are mass * length$^2$ * time−2−2^{-2} and the cgs factor is 1. The dimensions of Msun/Mpc33^3 are mass / length33^3 and the cgs factor is about 6.8e-41.
  4. Nov 2017
    1. Make full-text and cited references available via API. If these products were of equivalent or superior quality to those produced internally by ADS, it would simplify their workflow to rely on these APIs.

      Seems like open common development of tools to parse/flatten/process latex manuscripts is warranted.

    2. Currently, since arXiv lacks an explicit representation of authors and other entities in metadata, ADS must parse author metadata from arXiv heuristically.

      It will be interesting if solving this problem becomes one of hardcore ORCID integration coupled with metadata extraction from submitted manuscripts.

    3. ADS shares those matches with us via its API, and we use that information to populate DOI and JREF fields on arXiv papers.

      I've always wondered if this were true. I continue to wonder if arXiv uses other sources of eprint-DOI matches to corroborate or append to those from ADS.

  5. Aug 2017
  6. Jun 2017
    1. Common Astronomy Software Application package

      The software can be found on the software project website: https://casa.nrao.edu/ . This is a very limited description of the software package, its version, or its dependencies.

    2. AST-1312950

      NSF Grant, "Exploring Galaxy Evolution and Missing Satellites with ALMA and Gravitational Lensing" -- https://www.nsf.gov/awardsearch/showAward?AWD_ID=1312950

    3. #2016.1.01293.S

      The data for this ALMA observation can be obtained at this dataset link: http://almascience.nrao.edu/aq/?project_code=2016.1.01293.S

    4. ADS/JAO.ALMA#2015.1.00504.S

      The data for this ALMA observation can be obtained at this dataset link: http://almascience.nrao.edu/aq/?project_code=2015.1.00504.S

  7. Dec 2015
    1. It would be really cool if there were a "Sky" search mode next to the current set of Classic, Modern, Paper.

  8. Mar 2015
  9. iopscience.iop.org iopscience.iop.org
    1. The huge problem with floating topics is that they float.

    2. Geneva group “high” mass-loss evolutionary tracks

      Is there a http link for these evolutionary models?

  10. Dec 2014
  11. Nov 2014
    1. The word "data" is plural and takes a plural verb.

      It is what it is.

      Image Description

    2. manuscript

      Does the term "manuscript" still work for born digital and fully digital documents? Remember, there are no print editions of AAS journals as of 2015!

    3. I'm doing a collaborative annotation of this page to see if a) people want to give feedback on the utility of these instructions and b) to see if anyone wants to collaboratively annotate a document.

    4. Online-only Figures Online-only figures are intended to provide supplementary information that is not critical to the scientific content of the paper but that provides additional useful information for the reader. They are not allowed when the figures are an integral part of the paper, or simply to limit page charges. Such materials will carry a nominal publication charge depending on the number and size of the figure files, but again this will be a small fraction of the cost of printing the same volume of material. Note that online-only materials are subject to the same peer-review standards as the rest of the manuscript, and their inclusion should be justified on scientific grounds.

      This entire section has to be re-written because

      1. everything is an "online-only"figure.
      2. there is no printing.
      3. we now use "quanta" not "page charges"
    5. In the printed paper, the placement of tables will be determined by their first mention in the text.

      There is no printed version...