Bioblast manual

Topics alphabetical

Abstracts

• Abstracts are composed of two templates, abstract and labelling.

• 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.

• Abstracts should adhere to coherent formatting guidelines.

Addresses

Format for cities

• Format for city name in Form:O2k-Network Lab

• English city names are preferred: e.g. München is written as 'Munich', Wien as 'Vienna'.
• No punctuation: e.g. 'St Petersburg'
• Double city names: Hyphenated double names (e.g. Aber-Nein) are written as 'Aber-Nein'; if double names are separated by a space (e.g. Rio de Janeiro) use the space, 'Rio de Janeiro'.
• Double city names with lower case letters: use lower case as 'Rio de Janeiro'.

Figures

Format of figures

• Several figures do not change size when the zoom of the screen is modified, hence they change in proportion with the text. In many cases, a zoom of 125% is considered as a standard [Ctrl-O]. Therefore, formatting of such figures should be optimized at a zoom of 125%.

Pictures

Uploaded pictures should not have more than 1200px on the longest side. Profile pictures of persons should have this ratio: 3:4.

Persons

Format for persons

• Format for person names in Form:Person
• Format for author names in Form:Publication
• Format for person name in Form:O2k-Network Lab

• Family name_Initials (no punctuation). The initials should be confirmed from publications, such that author names and person names are linked.
• Double first names: no spaces and no hyphens are used, e.g. Jean-Pierre Mazat is written as 'Mazat JP'.
• Double family names: Hyphenated double names (e.g. Aber-Nein) are written as 'Aber-Nein'; if double names are separated by a space (e.g. Aber Ja) use the space, 'Aber Ja'.
• Special letters (umlauts or accented letters) should be written as: ä=ae, ö=oe, ü=ue, é=e; â=a; æ=ae, å=aa, ø=oe.

Creating a Bioblast person profile

1. create Mueller EF

• type “Mueller EF” into the search bar ->search

• create the page “Mueller EF” on this wiki ->click

• edit, type in "{{Person}}"

• edit with form, fill in person profile information

2. create Mueller Engelbert F

• edit, type in #REDIRECT Mueller EF

• create Mueller Engelbert: again #REDIRECT Mueller EF (optionally, if person uses this name too)

This puts the focus on the central profile page Mueller EF while all redirects are possible and do not interfere with the system.

Profiles With Wrong Redirects:

If you run across old redirects, i.e. Hauser Daniel as the main page and Hauser D with a redirect to Hauser Daniel, please correct them according to the following procedure:

1. Hauser E: DELETE

2. Hauser Daniel MOVE to Hauser E

References (Publications)

Edit references

• Epub ahead of print - Update citation
• In prep - Update; see free text for comments

Format of references

• Format for references in Form:Publication. »O2k-Publications and abstracts help

Article name (name of reference): 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:

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 Oxygraph-2k data, do not enter the O2k-Network lab (otherwise the reference will be listed as an O2k-publication)

Labelling references

• If you add a reference quickly to Bioblast without completing the labelling, add the term 'Labels' to 'Additional labels'. These references can be sorted automatically for later quality control of labeling.

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:* xxxxProperty "Allows value" is a declarative property and can only be used on a property or category page.

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

Automatic Tables

If you want to create an automatic table you have to write down the next code (adapting it to your necessities), after the code you would find the explanation to each part.

{{#ask:[[Category:O2k-Workshops]] [[Additional label::IOC]] |?Has title=Reference |format=broadtable |limit=500 |offset=0 |sort=Was written by |order=descending}}

• #ask:[[Category:xxx]] will search on the category where the information is, you can search over more than one category, for that you have to write:#ask:[[Category:xxx]][[Category:xxx]]

• [[Additional label::xxx]] in this area you have to write what you want to search, in which field, for example those pages that in the keyword field contein O2k and are from year 2012 -->[[Keyword::O2k]][[Year::2012]]

• |?Has title=reference |?Was published in year |?Diseases With the question mark you selected the fields you want to appear in the table

• |format=broadtable |limit=500 |offset=0 this line define the format of the table. it´s necessary to write limit 500 because if it´s too short it would not appear all of them.

• |sort= Was written by |sort=was published in year |sort=Has title |sort=Was submitted in year Here you selected the field from which the table will be sorted.

• |order=descending or ascending}} choose one of both options to order the table.

Attention-

• For automatic publication tables sort by Was published in year / for automatic abstract tables sort by Was submitted in year
• If in the pages where you are searching to create the automatic table, exist the label articletype, this page WILL NOT appear in the table.

O2k-Workshop Websites

» O2k-Workshops Template

Startpage

Changing the startpage of the wiki/ the link of the logo in the navigation bar: Edit the page “MediaWiki:Mainpage”, write inside the name of the page you want to have as the startpage. Save.

Link: "skins/Vector.php"