Bioblast manual

Topics alphabetical

Abstracts

• MiP2013 Abstracts; Prep: Talk:MiP2013 Abstracts

Addresses

Format for cities

• Format for city name in Form:MiPNetLab

• English city names are preferred: e.g. München is written as 'Munich', Wien as 'Vienna'.
• No puncutation: 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%.

• Example: 933px in OroboPedia Template:Mainpage welcomebox title.

Persons

Format for persons

• Format for person names in Form:Person
• Format for author names in Form:Publication
• Format for person name in Form:MiPNetLab

• 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.
• Please see Discussion for more clarity

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.

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. After 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.
3. If you add a publication, that does not include Oxygraph-2k data, then do not enter the MiPNet lab (otherwise the reference will be listed as O2k-publication)

Labelling references

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

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 (if this property hasn´t got 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 them in edit 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 wanted 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 don´t 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