Help:Publications and abstracts

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Section editors

Tasks

  • PLoS One changed the style in writing already in 2012: any impact for our list in the bioblast? correct now: PLOS ONE
~ Lanerv 23:05, 26 January 2016 (CET)
  1. It's still "PLoS One" on PubMed, which is what we adhere our formatting to, but i don't mind changing it to "PLOS ONE" in the future and with the old entries (possible task for Lisi?)
~ Kandolf Georg 09:25, 9 February 2016 (CET)
  1. And it is still even "PLoS ONE" on the PLoS ONE website. Box: "Citation: Kiely B, Migdal TR, Vettam S, Adesman A (2016) Prevalence and Correlates of Elopement in a Nationally Representative Sample of Children with Developmental Disabilities in the United States. PLoS ONE 11(2): e0148337." Gut, dass sich jemand um die wirklich wichtigen Dinge kümmert...Krumschnabel Gerhard 14:29, 11 February 2016 (CET)
  • A policy decision is required as to whether we label the theses as "Doctoral Thesis" (see Hanson 2007) or PhD Thesis. My suggestion would be "Doctoral" as it covers Dr rer nat, for example and MD.
~ David
  1. Or keep it totally general as 'Theses', and add the PhD etc in the citation. ~ Gnaiger Erich 21:07, 7 March 2012 (CET)
  2. "Thesis" (spelled with "i") in the page name and academic title in the reference appears reasonable. ~ Kandolf Georg 08:19, 29 January 2016 (CET)

Filters and values (keywords) in filters: Towards a strategy / Questions

  • Discussion about how to handle changes in Bioblast Publications - e.g. adding properties, deleting properties...
  • Problem: how to realise if a paper has been adapted to the changes or not?
  • These points need to be updated:
  • At the beginning: in prep and edited will be free
  • After editing: "in prep" or "edited" will be ticked

Injuries and Adaptions

  • 'Cancer; Apoptosis; Cytochrome c' -> 'Cancer'; 'Apoptosis'


Add references (publications; O2k-Publications) and abstracts

In the spirit of Gentle Science and Open Access, we invite you to use the Bioblast wiki to add


Login and edit

  • You may edit your entries on the website at any time. Check for deadlines for printed versions of abstracts for workshops or conferences.
  • Access your reference or abstract page (search for familiy name using the search box, right top) and click on the Edit with form button (upper toolbar, right) to access the editing mask of your abstract or reference.
O2k-Network Labs: O2k-Publications and abstracts from an O2k-Network Lab - enter the respective UserCode(s) (e.g AT_Innsbruck_Gnaiger E). If you do not remember the code, check here for a list - Category:O2k-Network.


Authors

  • Authors: Adhere to the following format: lastname + initial firstname (e.g Mueller M), authors' names separated by comma (,), no "and" or "&", umlauts or accented letters should be written as: ä=ae, ö=oe, ü=ue, é=e; â=a; æ=ae, å=aa, ø=oe.
  • In the reference, special characters of authors should be kept (for the use search function).


Labelling

  • If you add a reference or abstract quickly to Bioblast without completing the labelling, add the term 'Labels' to 'Additional labels'. These pages can be sorted automatically for later quality control of labeling.
  • When you add a new reference (O2k-Publications), list the current year and month under additional labels in the format YYYY-MM (e.g. 2017-07). This helps us in keeping the new recent_O2k-Publications page updated.
  • Additional labels
  1. ORO (= Oroboros Events)
  2. IOC (= O2k-Workshops)
  3. O2k-Network (= IOC at O2k-Network Laboratories)
  4. MitoCom (= Talk:MitoCom O2k-Fluorometer) - discontinued, has been replaced by:
  5. MitoFit
  6. MITOEAGLE (for events which may be specifically supported by the COST Action)
  7. 2014, 2015... (= year of event, all)
  8. Next (= upcoming events, for ORO and IOC)
  9. TRACT (for events within the TRACT project)
  10. TRANSMIT (for events within the TRANSMIT project)
  11. mtFOIE GRAS (for events within the mtFOIE GRAS project)
  12. Labels (labeling has not yet been done or should be checked -> four eyes)
  13. noPDF (publication has been entered solely based on the abstract)
  14. date. e.g. 2017-05 (date of implementation, used to generate Recent O2k-Publications table


Preview and save

  • Preview does not work if [Edit with form] is used. After saving, use [Edit] for further steps. Scroll to the bottom of the page and click [Show preview]. For saving the changes at the end of your session, click [Save page].


Abstracts

  • To create a new abstract page access the abstract form and enter the abstract's title using the format Surname year abstract event (e.g. Amoedo 2013 Abstract MiP2013, Gnaiger 2014 Abstract ASMRM2014 or Fasching 2013 Abstract IOC79).
  1. Save and then edit again to complete the entry.
Update (2017-06-19): abstract page titles simply contain author's lastname, year and event, e.g. Garcia-Souza 2017 MiPschool Obergurgl
Background: this format makes it easier to export participant lists.


Text and references

  • We recommend preparing abstract texts in a text-file and then simply copy- and pasting the text to the input mask on the website.
  • Text formatting use paragraphs but no subheaders for 'Introduction', 'Material and Methods', ect.; format latin terms such as in situ in italics; if the number of words exceeds 500, continue the abstract in the free text box at the bottom of input mask.
  • References: Quote references in the text by numbers in brackets [1]. All authors are listed in numerical series without punctuation and are separated by comma (,); no "and" or "&". Use capitals only where necessary in reference titles. Use the shortest possible format for page numbers.
Reference format sample:
  1. Pesta D, Gnaiger E (2012) High-resolution respirometry. OXPHOS protocols for human cells and permeabilized fibres from small biopisies of human muscle. Methods Mol Biol 810:25-58.


Authors and affiliations

  • Authors: Author names without special characters.
Umlauts or accented letters should be written as:
ä=ae, ö=oe, ü=ue, é=e; â=a; æ=ae, å=aa, ø=oe.
  • Format: Lastname + Initials firstnames (e.g Mueller M)
  • Different Author names are separated by comma (,), no "and" or "&",
  • Affiliations and author contributions: Enter all relevant information below this header at the bottom of the abstract page (free text). Avoid any conflict with copyrights.

Publications / References

Page name: Author_Year_Journal
  • Author: The most constant part of the author name is the family name. For the same author, initials may vary occasionally between one or more initials. Hence, reduction to the family name.
  • Year: The year may change from the original year of Epub to the final year of publication. Then the article has to be moved to a new name.
  • Journal: Journal abbreviation (without punctuation) Volume:123-4.
  1. (As of 2011-Nov-21) The journal abbreviation in Bioblast follows exactly the format of the journal abbreviation used in Pubmed (exception: no final dot is permitted in Bioblast). Consequently, the punctuation in the journal abbreviation is also omitted in the full reference.
There were initially two other formats for the Journal in the article name on Bioblast:
  1. (Until 2011-Oct) A short 'slang' acronym, such as JEB, to keep the article name short. No standardization is possible, since not all journals have commonly used 'slang' acronyms, and the acronym is different from the standardized abbreviation used in the full reference.
  2. (Until 2011-Nov-21) Standardized abbreviation, with punctuation, as used in the full reference until Nov 2011, such as J. Exp. Biol. The final dot in the article name, however, is truncated when the weblink is copied, such that the copied weblink becomes dysfunctional.
  • Volume and page numbers:
  1. (2014-06) Volume number followed by colon followed by full first page number (without space)-truncated last page number. Example: 324:H1272-9.
  2. (before 2014-06) Volume number followed by colon followed by space followed by full first page number-full last page number. Example: 324: H1272-H1279.
  • If you add a publication that does not include O2k data, do not enter the O2k-Network lab (otherwise the reference will be listed as an O2k-publication)
Link: Provide a weblink of interest here, preferably a PubMed link. Sample: PMID: 24263979. If an open access PDF file is available via that link add "Open Access" PMID: 24263979 Open Access
  • If a publication is available Open Access via PubMed, format guideline for the PMID code is as follows: PMID: 25749501 Open Access
  • If a pdf is not Open Access but is made availabe on Bioblast, format guideline is as follows: PMID: 24242424 Bioblast pdf


Keywords: Enter a list of keywords. Keywords start with a capital letter and are seperated by comma (,).
Labels: Please tick the appropriate "keywords" in the following boxes, to make sure that the added or edited publication appears automatically in the specific filters. For help in interpretating labels correctly, check the MiPMap
  • Additional labels: When you add a new O2k-Publication), list the current year and month under additional labels in the format YYYY-MM (e.g. 2016-01). This helps us in keeping the Recent O2k-Publications page updated.
  • [Epub ahead of print] - for screening of entries which need updates.
Free text: Enter additional information here.

Generate a new line for labeling: MiPMap Publications and Abstracts

Template

Template:Abstract


Forms

Form:Abstract

! High-resolution respirometry:

| instruments

|-

! Event:

| event

|-

Template:Labeling

Template:Labeling

|instruments=

|event=



Filters

Filter:High-resolution respirometry

This filter covers the property Instrument and method. It has the label High-resolution respirometry.

Filter:Events

This filter covers the property Event. It has the label Event session.

Properties

Property:Event

This is a property of type String.

The allowed values for this property are:

  • A1
  • ...

Labels of publication (Add or delete)

1 Special pages/Filter: a Delete: Choose the filter you want to delete and click on the property which the filter refers to (if this property does not have any values it never would appear on Special pages/properties. i.e: Filter xxxf

-a.1 Delete the property of the selected link (delete page) i.e: xxxpage
-a.2 Delete the filter ie: xxxfilter

b Add:

-b.1 Special pages/Semantic Drilldown/Create a filter : Name and select the property that this filter covers.
-b.2 Special pages/Semantic form/Create a property: as string, save and the edit and add the values i.e:* xxxx

2 Special pages /Templates: Publication (num 44) and click on its define category Publications. Edit and delete or add (depending the case) *Filter xxxfilter

3 Special pages/Form/Publications: Select edit

- 3.1 scroll down and delete or add the name you want to appear and the name of filter or property in field

i.e: ! MiPareas: | area |-

- 3.2 if you want to change the name that appears where MiPareas is, wrote the new one. i.e: !MiPareas_new

4 Special pages/Form/Abstracts:delete the property or add/ change a new property writing i.e: !New_property

5 Special pages/Template /labeling:

- 5.1 Delete or add the property name on

''{{Labelling |new property to add }}''

- 5.2 Scroll down to delete (or add) the array

i.e: {{#if: {{{filtername|}}} |'''name to appear on the table:''' {{#arraymap:{{{filtername|}}}|,|x|[[Property::x]]}} }}''


NOTES:

- Form use templates

- Filter and properties do not accept & or - or , always separate the long name with ;

- Automatic tables: they make a search to show the data, if you change, create or delete a new property. go to edit on the automatic table and delete or change the name on #ask xxxpage


The following sections must be integrated/updated/deleted

O2k-Publications

  • Add a new reference
  • To add a new reference access the Publication submission form and follow the instructions on the page or here
  • When you add a new reference (O2k-Publications), list the current year and month under additional labels in the format YYYY-MM (e.g. 2016-01). This helps us in keeping the recent O2k-Publications page - which should always show O2k-publications put online within the last two calendar months - updated. (strategy as of 2016-01)
  • If a publication is available Open Access via PubMed, format guideline for the PMID code is as follows: PMID: 25749501 Open Access
  • If a pdf is not Open Access but is made availabe on Bioblast, format guideline is as follows: PMID: 24242424 Bioblast pdf
  • Use [Epub ahead of print] at the end of a reference to indicate that issue and page numbers were unknown at the time of adding. Also mention [Epub ahead of print] under additional labels. This makes it easy to filter for entries that need editing later.
  • Type "labels" under additional labels to indicate that labeling might need revision or has not been done at all. Experienced labelers remove "labels" after revising labeling
  • Creating or deleting labels:
  • All current (2016-02) root-category O2k-Publication labels = properties which divide up into more individual labels:
  1. http://www.bioblast.at/index.php/Property:MiPareas
  2. http://www.bioblast.at/index.php/Property:Mammal_and_model
  3. http://www.bioblast.at/index.php/Property:Nonmammal
  4. http://www.bioblast.at/index.php/Property:Tissue_and_cell
  5. http://www.bioblast.at/index.php/Property:Cell_line
  6. http://www.bioblast.at/index.php/Property:Preparation
  7. http://www.bioblast.at/index.php/Property:Enzyme
  8. http://www.bioblast.at/index.php/Property:Stress
  9. http://www.bioblast.at/index.php/Property:Diseases
  10. http://www.bioblast.at/index.php/Property:Respiration_and_regulation
  11. http://www.bioblast.at/index.php/Property:Coupling_states
  12. http://www.bioblast.at/index.php/Property:Substrate_states
  13. http://www.bioblast.at/index.php/Property:Instrument_and_Method
  14. http://www.bioblast.at/index.php/Property:Additional_label
  • To create or delete labels enter and adapt Properties
  • Labels cannot be re-named. A new label needs to be introduced, all old ticks removed, new ticks made and then the old label deleted.
  • Alternatively
  1. Go to: http://www.bioblast.at/index.php/Special:BrowseData/Publications and select all existing publications with the "value" you would like to change/delete. (e.g. you would like to separate the value "Permeabilized Cell or Tissue; Homogenate" of the property "Preparations": http://www.bioblast.at/index.php/Special:BrowseData/Publications?Preparations=Permeabilized_Cell_or_Tissue%3B_Homogenate)
  2. Press [Strg+C] and copy the page into an Excel sheet by [Strg+V] - by doing this you have a back-up with functioning links to all the pages that include this "value".
  3. Go to the corresponding property and change/delete/define new values: http://www.bioblast.at/index.php/Property:Preparation and "Save page"
  4. Now all pages that previously contained the "old value" will show a small yellow exclamation mark.
  5. Go to the Excel sheet and open the first page by the weblink.
  6. "Edit with form"
  7. Select the "new value" and "Save page".
  8. Now the "new value" is selected and the "old value"/the exclamation mark is gone.
  9. Pages from the "Excel Back-up" have to be opened with "Edit with form" and "saved" to make the changes active!
updated ~ Kandolfg 09:37, 16 February 2016 (CET)
  1. To add a table with publications published in e.g. 2013, create a page called O2k-Publications_2013 and copy the text below (inline query) into the edit form.
  2. Now all publications that have the label Oxygraph-2k and were published in the year 2013 are listed automatically on this page.

Back to: '''[[O2k-Publications|Chronological Reference List]]''' {{#ask:[[Category:Publications]][[Was published in year::2013]][[Instrument and method::Oxygraph-2k]] |?Was published in year=Year |?Has title=Reference |format=broadtable |limit=500 |offset=0 |sort=Was written by |order=ascending }} [[Category:Publications]]

  1. To create an automatic list of O2k-Publications on a specific topic, create the page name (e.g http://www.bioblast.at/index.php/O2k-Publications:_Isolated_Mitochondria O2k-Publications:_Isolated_Mitochondria) and copy the text below into the new page.
  2. Here the list contains the property Preparation and only shows publications with the value Isolated Mitochondria
  3. http://www.bioblast.at/index.php/Property:Preparation

Back to: '''[[O2k-Publications: Specific topics]]''' {{#ask:[[Category:Publications]] [[Preparation::Isolated Mitochondria]] [[Instrument and method::Oxygraph-2k]] |?Was published in year |?Has title |?Tissue and cell type |format=broadtable |limit=150 |offset=0 |sort=Was published in year |order=descending }} [[Category:Publications]]

  • Change the text that is displayed when clicking on "add reference" here
  • or by accessing: Special:AllMessages, filtering by prefix: Publication, clicking on EDIT and modify.
http://www.bioblast.at/index.php/Editors_O2k-Publications
  • Recent O2k-Publications

Manually update the Recent_O2k-Publications at the beginning of a every month by changing the query [[Additional label::2016-02]] OR [[Additional label::2016-03]] to the last and current month.


Abstract pages

  • Participants of events and workshops send abstract to: instruments@oroboros.at
  • Specific formatting guidelines for abstracts send as Word documents for workshops and meetings and MiP conferences are online and links should be provided for participants in advance.
  • Wherever possible (events, workshops, ...), abstracts should include the participants' photo.
  • Abstract are submitted to the Bioblast wiki as follows:
  • Update (2017-06-19): abstract page titles simply contain author's lastname, year and event, e.g. Garcia-Souza 2017 MiPschool Obergurgl
  • Background: this format makes it easier to export participant lists


Contributed by ~ Kandolfg 15:03, 15 February 2016 (CET)