Histri manual
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April 28, 2008
Make Histri
We want to reconstruct the exchange history of colonies of the same strain
between culture collections (“histri”)
Figure: No histri information
Figure: Histri built
The histri tool helps you in this proces!
Histri manual
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2/23
Terminology
Culture a colony of a certain strain, held at a specific collection
Synonym an alternate name for a culture (e.g. name with a typo)
Strain a collection of cultures of the same “kind”, i.e. originating
from the same isolate
Cultures vs. strains
A strain consists of multiple cultures. We work with one strain at a time:
we reconstruct the histri by finding the predecessor of each culture.
A culture and its synonyms are grouped in a block. We will build the tree
using these blocks.
Histri manual
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3/23
Overview
1
Introduction
2
Basic use
3
Where to find the history information
4
HistriSuggest
5
Advanced features
6
Wrap-up
Histri manual
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4/23
Creating the tree
Easy: drag and drop
Drag a block over its new parent and drop it!
If you use the right mouse button, you can also choose to add the
culture as a synoym
Removing a child
Drop the child on white space
Cultures which are not in a tree are placed under the tree in a grey
rectangle
Histri manual
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Navigating the tree
Clicking a culture selects it and unfolds information about the culture
Right hand side
Strain tab global information
about the strain
Culture tab specific info on the
selected culture (and transfer
from predecessor)
At the bottom
Culture Table tab contains a list
of all cultures in the strain
History provenance tab shows
overview and analysis of history
strings
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Annotating the tree (Culture tab)
Each transfer can be annotated with five fields. A transfer with
annotations is drawn with a thicker line.
Check box checked: this information
is unknown
You need to uncheck the checkbox
to enter information
Histri manual
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Annotating the strain (Strain tab)
Each strain can be annotated with 7 fields
Isolate can be set
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By selecting a culture and clicking on the star button
By right clicking on a culture and using the popup menu
Annotation is important
Please annotate the edges and the strain as much as possible: it is
impossible to do this annotation automatically.
Histri manual
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Save
Save
You can enter a message
Use it to report inconsistencies, errors or strange situations
Figure: Standard message if the histri is saved for the first time
Histri manual
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9/23
Overview
1
Introduction
2
Basic use
3
Where to find the history information
4
HistriSuggest
5
Advanced features
6
Wrap-up
Histri manual
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10/23
Where to find history information
In the catalogs of the collections
Online Browsing the online catalog
Use StrainInfo!
By double clicking on a culture
By selecting a culture and clicking on the world button
Built-in Textual descriptions copied from the online catalogs
Can be viewed in the Culture table
Analysis in the History provenance tab
Drawback: is not complete
Paper editions Found in the library
Sometimes more elaborate as the online catalog
Describes the view in the past (information can have
been changed)
Histri manual
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Culture table
Is a list of all cultures in the strain
Shows textual history description and some exta information
Has powerfull a filter bar (as e.g. in outlook)
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Entering a keyword directly starts a search
The search looks for matches in all columns (including history
description)
Only matching cultures are shown in the list
Filter bar works case insensitive by default
Extra filters for cultures with history descriptions and cultures not yet
in tree
Can be used to make cultures invalid (by unchecking the valid flag)
Figure: Culture table
Histri manual
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History provenance tab
Shows analysis (including identification) of history descriptions
Identified culture names are hyperlinked and colored
Green current selection
Red predecessor of current selection (if exists)
Grey identified culture
Clicking a hyperlink selects the culture
Figure: “Show one” mode
Histri manual
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History provenance tab
Can be used in three modes
Show all lists all history descriptions in strain
Show filtered show only history descriptions with matches on selected
culture or predecessor
Irrelevant parts of the string are omitted
Show one displays only one history description
Can be used to check all history strings
Browse using Previous and Next
You can switch modes using the hyperlinks at the bottom of the list
Figure: “Filter on selection” mode. Note that not matched struts are not shown.
Histri manual
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14/23
Overview
1
Introduction
2
Basic use
3
Where to find the history information
4
HistriSuggest
5
Advanced features
6
Wrap-up
Histri manual
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15/23
What is HistriSuggest?
HistriSuggest tries to suggest possible parents
Possible predecessors are shown with a red border
Possible synonyms are shown with a red dashed border
These suggestion are based on
Cultures identified in textual history description
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Identified cultures can be seen on the History provenance tab
Domain knowledge
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When collections were renamed, merged or incorporated into others
Side effect: original collection is sometimes not listed in textual
descriptions
A “looks like” heuristic (for synonyms)
See provenance (slide 20)
Histri manual
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AutoBuild
These suggestions can be used to build the tree automatically
Using the magic wand tool
When multiple possible predecessors are suggested manual resolution
is necessary
This only makes your task easier and faster, but does not replace you!
You are irreplaceable
Correctness needs to be checked and incompleteness needs to be
completed. This is not possible without manual curation. Thank you for
your help!
Histri manual
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17/23
Overview
1
Introduction
2
Basic use
3
Where to find the history information
4
HistriSuggest
5
Advanced features
6
Wrap-up
Histri manual
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18/23
Highlight system
The highlight system can be used to highlight cultures which have a
certain property
Have a page in an online catalog
Have a (built-in) history string
Have at least one suggestion
Are shown in the Culture table (especially handy when combined with
the filter)
...
Highlights can be enabled using the toolbar or the menu
When multiple highlights are enabled, they are combined
Histri manual
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Provenance
Provenance = the proof of automatically generated information
Can be viewed for each culture with a suggestion
Usually is a combination of multiple objects
Each object has a “trust value”
You can open a dialog by clicking the eyes button
Different kinds of provenance
Domain knowledge
Derived from history descriptions
Heuristic “looks like”
Translation to synonym
Combine domain knowledge with conflicting history string knowledge
Combined positive knowledge (with possible negative provenance)
Histri manual
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Tools
Special tools
Reload reloads the histri without saving
Destroy removes all edges
Add culture adds a new culture
Zooming
Using the mouse wheel
Using the “zoom in” and “zoom out” buttons on the toolbar
By using
Histri manual
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21/23
Overview
1
Introduction
2
Basic use
3
Where to find the history information
4
HistriSuggest
5
Advanced features
6
Wrap-up
Histri manual
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22/23
Checklist
How to build a histri
1
Load a strain
2
Build using AutoBuild
3
Check correctness
4
If necessary, insert new cultures
5
Group all synonyms
6
Manually connect left cultures
7
Annotate as much as possible (check all catalogs)
8
Do not forget to save
9
Report irregularities
Histri manual
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23/23