amo database query interfaces february 1, 2006

February 1, 2006

AMO Database Query InterfacesFebruary 1, 2006

Here are some notes on screen layouts for AMO database queries. Hopefully this document will give interface designers a start on developing web pages for database access. I included both our open ideas about user interface as well as specific layouts to start developing screens. See the later slides (starting with #6) for proposed screen layouts. =pg

February 1, 2006

Screen Flow: Query - List - Detail

Query

List

Detail

Starting point for data request; for example:• Select all the sequences for a specific location• Select all sequences from low pH soils• (many more criteria available … )

Displays multiple results that meet query criteria• Enables scrolling and paging through multiple

results• Enables download of the entire set of results to a

text file (fasta)• Enables selecting an individual sequence to

proceed to the detail screen.

Displays all data for a single selected sequence• Also provides access to detailed location and sample

information• Can link to more details such as geochemistry• Can navigate back to Query or List screens so user

can revise choices and look at other sequences

The diagram below represents the screen flow that is common throughout AMO database access queries. This presentation focuses on the example of sequence data because sequence is a major focus of data gathering and investigation. However, a similar flow will also apply for direct query of location, sample and geochem data.

February 1, 2006

Spatial (GIS) Queries: Query - List - Detail

Query by Attribute

List

Detail

Query by attribute is the common database query based values of data in the database. For example, select all sequences gathered on a specific date.

GIS queries can use the same list and detail screens as attribute-based database queries.

Query by Location

GIS or “spatial data” queries use location to select information. Examples: select sequences found within 1 meter of a given location; or, select sequences found within the bounds of a specific vegetation type.

Spatial queries and queries by attribute may be combined.

Spatial queries can feed to the same list (and detail) screens used by queries by attribute.

February 1, 2006

Screen Data: Sequence Query ScreenThere are at least three approaches to the initial query screen. We can consider all of them for AMO and then determine which best suits our goals. The following slide recommends an approach for AMO.

There’s a “pre-defined” query approach that SIMO uses, where many query options are provided to the user in table form. These are “pre-defined” in that they are a much smaller set than a truly open-ended query definition. The defined queries reflect (perhaps) the most likely queries users might want. For example, see (http://simo.marsci.uga.edu/public_db/data_matrix_env.asp).

A corresponding approach for AMO would be to anticipate what we think are the likely major categories of queries, and provide a similar interface for those queries in a pre-defined form.

“Open” queries give the user tools, using menus or buttons, to select their own parameters for a query. SIMO uses an extreme form of open query to complement their predefined queries, that allows users to define a very wide range of choices, but requires significant technical knowledge (http://simo.marsci.uga.edu/public_db/custom_fasta.htm).An aspect of MaNIS is the ability to select from a concept list - an open query with a limited set of user options.(http://manis.mvz.berkeley.edu/pres/PresentationServlet?action=menu&loc=http%3A%2F%2Fbnhm.berkeley.museum%2Fmanis%2FDwC%2Fdarwin2jrwInfodo.xml&reqType=search)

1 2

Finally there are joint queries that span more than one database. MaNIS uses this (also on http://manis.mvz.berkeley.edu/pres/PresentationServlet?action=menu&loc=http%3A%2F%2Fbnhm.berkeley.museum%2Fmanis%2FDwC%2Fdarwin2jrwInfodo.xml&reqType=search). AMO will want to include this in our interface, though I recommend we develop our single database interface first.

3

February 1, 2006

Screen Data: Sequence Query ScreenThe initial query approach recommended for AMO is an open query giving the user options to select on parameters of location name, sample date and geochemical characteristics of sample locations.

• Eventually all three types of queries (see previous slide) may be required.

One way to implement this would be drop-down menus for each choice:

Location Name

<list of choices>

Sample Date

<list of choices>

Geochemistry

<list of choices>

Select …

Other forms of buttons or menus may be preferred. In addition, I’m sure we’ll refine our list of parameters and choices to offer as we proceed with implementation.

February 1, 2006

Screen Data: Sequence List Screen

Location ID Location Name AMO Sequence Name

GenBank Accession #

Bases Sample ID Sample Date

location.locationID

location.locName sequence.sequenceName

sequence.GenBankNumber

sequence.pairs

soilsample.soilsampleID

soilsample.sampleDate

0000001 Talus site north probe

T3_A_C1 AY999999.9 648 0000001 2000-07-17

0000001 Talus site north probe

T3_A_D1 AY888888.8 659 0000001 2000-07-17

0000002 Talus site data logger

T0-D3 AY555555.5 681 0000002 2001-08-21

0000002 Talus site data logger

T0-D12 AY444444.4 784 0000002 2001-08-21

Below is a sample layout for a sequence list screen. This sample is completely unformatted; all AMO styles are yet to be applied. Also, since we are in preliminary design, the actual fields desired for this screen will probably change as we refine our design. However this represents a general format for the sequence list display. Note the second row (shaded) which indicates the data element to populate each column (the format is “tablename.columnname”). The following four rows provide some sample data to illustrate the example.

Note that some data elements are formatted to indicate they are hyperlinks (blue, underlined). Clicking on a link for “AMO Sequence Name” takes the user to the detail screen for that sequence. Clicking on the GenBank Accession link goes to the corresponding external link for the GenBank information on that sequence.

It may be desirable to make many other fields on this screen sortable and linkable, e.g., click on “Location Name” to see detail about that location OR to select all sequences for that location. (design details still open)

Also useful on this screen:1) A reminder for users that displays the criteria they chose from

the query screen that brought them to this point. (For example in a header position or other highlighted format)

2) A link or button to download ALL the sequences in this list to a text file (fasta format). May require dialog box to choose location for the downloaded file.

This screen also needs navigation buttons (previous, next, first, last) to handle cases where there are multiple screens worth of records in the list.

February 1, 2006

Sequence Detail Screen Alternatives

Sequence Detail

A concise sequence detail screen has inks to detail screens for location and sample (also able to link back to screens - the arrows are two-way)

There are (at least) these two options for laying out the sequence detail and providing the user access to additional detail relevant to the sequence.

Sample Detail

Location Detail

Sequence

Detail

---------

Sample

Detail

----------

Location

Detail

link-to

A long sequence detail screen requires page-downs but includes sample detail and location detail on that same screen. (E.g., SIMO uses this form)

hAlternative#1

Alternative#2

February 1, 2006

Screen Data: Sequence Detail Screen

16s rRNA Gene Sequence for sequence.sequenceName

sequence.sequenceFormat: lay the sequence out in column and row format: each row of base pairs has 6 blocks of 10See (http://simo.marsci.uga.edu/public_db/matrix_details_env.asp?id=1068&match=) for an example of this layout.See next slide for an example sequence.

Number of base pairs= sequence.pairs

GenBank Integer ID sequence.GenBankGI

GenBank Accession Number sequence.GenBankNumber

GenBank Defintion sequence.GenBankDefinition

Here is a sample layout for the sequence detail screen Much more data will be present on this screen after we implement phylogeny information; currently this is the basic layout for sequence data. See the following slides for some sample data in this format.

February 1, 2006

Sequence Detail Sample Data

16s rRNA Gene Sequence for T3_A_C1

GCTCACACCGATAGTCCCTCTAAGAAGTCGCGTCCAAAGGAAGAATCCTTTGTCGAACTATTTAGCAGGTCGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCACTCCACCAACTAAGAACGGCCATGCACCACCACCCACAGAATCAAGAAAGATCTTCAATCTGTCAATCCTTACTGTGTCTGGACCTGGTAAGTTTTCCCGTGTTGAGTCAAATTAAGCCGCAGGCTCCACTCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCGAATGAAGTCGAAAATGCAACGTTCACTCATCCCTAGTCGGCATAGTTTATGGTTGAGACTACGACGGTATCTGATCGTCTTCGATCCCCCAACTTTCGTTCTTGATTAAAGAAGACATCCTTGGTGAATGCTTTCGCATAAGTTAGTCTTCAGCGAATCCGAGAATTTCACCTCTGGCCGCTGAATACTAGCACCCCCAACTGTCCCTATCAATCATTACTTCAGTCCTAGAAACCAACAAAATAGAACCGAAGTCCTAAATTATTATTCCATGCTAATGTATTCATAGCATAAAGCCTGCTTGAAACACTCTAA

Number of base pairs= 648

GenBank Integer ID (not yet assigned)

GenBank Accession Number (not yet assigned)

GenBank Defintion (not yet defined)

This sample corresponds to line 1 on the “list screen” sample data slide.

February 1, 2006


16s rRNA Gene Sequence for T3_A_D1

CTTGAGCCAAAGTCCCTCTAAGAAGCTGGCGACCAACAAAAGTCAATCTAGCTATTTAGCAGGTCANGGTCTCGTTCGTTATCGCAATTAAGCAGACAAATCACTCCACCAACTAAGAACGGCCATGCACCACCACCCATATAATCAAGAAAGAGCTATCAATCTGTCAATCCTAAACATGTCTGGACCTGGTGAGTTTTCCCGTGTTGAGTCAAATTAAGCCGCAGGCTCCACGCCTTGCGCAATTTCTTAGGCTTGTAGCCTAAAAGCACGATCATATCTTAACGAATTACAATAATTCGACGACCTCCACTTGATCTGTGGACCCTAGAAGGGTTGCAGGTCAGCTATAAATGCCGTCCATGCAGTTAAAAGGTCTAACCGAGCGAATCGGTCATATAGGCACCACAAGAGTGGTTAATCTGGTGCCCTTCCGTCAATTTCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGAGCCCAAAAACTTTGATTTCTCGTAAGGTGCCGAACGGGGCATAAAAAACCACCGTCCGATCCCTAGTCGGCATAGTTTATGGTTAAGACTACGACGGTATCTGATCGTCTTCGATCCCCTAACTTTCGTTCACTGATTAATGAAAACATCCTTGGCGAATGCTTTCGCAATAGTTAGTC






February 1, 2006


16s rRNA Gene Sequence for T0-D3

ACACTGCTCTCTATCAGTCTTTGACTGTTACTGTGAGAAAATTAGAGTGTTTCAAAGCAGGCTATTGCAGGAATACATTAGCATGGAATAACGAACGTCTAGAATATTGGTTAATTCTAGATAACGATTAATAGGGACAGTTGGGGGCATTAGTATTTAATTGTCAGAGGTGAAATTCTTGGATTATTTAAAGACTAACGTATGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAAGAACGAAAGATAGGGGATCAAAGACGATCAGATACCGTCGTAGTCCTATCTATAAACTATGCCGACTAGGGATTAGGGTGGAAAAGTACCATCTTAGTACCTTATGAGAAATCAAAGTCTTTGGGTTCTGGGGGGAGTATGGTCGCAAGACTGAAACTTAAAGAAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGGAAACTTACCAGGTCCAGACGTAGTAAGGATTGACAGATTGATAGCTCTTTCTTGATTCTATGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGTGATTTGTCTGGTTAATTCCGTTAACGAACGAGACCTTAACCTGCTAACTAGACTAGTCCATTTTATGGATTCAGTCTTCTTAGAGGGACTATGTTGCGASAGCACAGGAAGTTTGAGGCAA






February 1, 2006


16s rRNA Gene Sequence for T0-D3

GTAGTTGGATTTGGATGGGTTGTTGCGGTCCGCTCTGGTGAGTACTGCTGTGGCCTATCTTTCTGCCGGGGACGGGCTCCTGGGCTTCACTGTCCGGGACTGGAGTGGCGATGTTACTTTGAGTAAATTAGAGTGTTCAAAGCAGGCNTACGCTCTGAATACTTTAGCATGGAATAACACGATAGGACTCTGGCCTATCTTGTTGGTCTGTAGGACCGGAGTAATGATTAAGAGGGACAGTCGGGGGCATTCGTATTTCATTGTCAGAGGTGAAATTCTTGGATTTATGAAAGACGAACTACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGATTAGATACCGTNGTAGTCTCAACCATAAACGATGCCGACTAGGGATTGGCGGATGTTTATTCAATGACTCCGCCAGCACCTTATGAGAAATCAAAGTTTTTGGGTTCCGGGGGGAGTATGGTCGCAAGGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGCGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAAACTTACCAGGTCCAGACATAGTGAGGATTGACAGATTGAGAGCTCTTTCTTGATTCTATGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGGTTGCCTTGTCAGGTTGATTCCGGTAACGAACGAGACCTCAGCCTGCTAAATAGTCCTAGTCGCTTCTTGCGGCTAGCTGACTTCTTAGAGGGACTATGGCGTTAGTCAAGGAAGTATGAGTTTGAGGCAA






February 1, 2006


16s rRNA Gene Sequence for (none)

GTGTCTTTCGACACTCGCCGGCTTTCACCGGTTTAGAGATGCATGTCAAGGCCTGGTAAGGTTCTTCGCGTTGCATCGAATTGAGCCACATACTCCACCGCTTGTGCGGGTCCCCGTCAATTTCTTTGAGTTTTAATCTTGCGACCGTACTCCCCAGGCGGCACGTTTAACGCGTTAGCTCCGGCGCAGAAGGGGTCGAATCCCCCCACACCAAACGTGCACCGTTTACTGCCAGGACTACCGGGGTATCTAATCCCGTTTGCTCCCCTGGCCTTCGTGTCTCAGTGTCAGGAACTGTCCAGAGACCCGCCTTCGCCGCTGGTCTTCCTTACGATATCTACGCATTTCACTGCTACACCGTAAATTCCAGTCTCCTCTCCAGTCCTCAAGCACGCCAGTATCGAATGCAGTTTCGGAGTTAAGCTCCGAAATTTCACACCCGACTTAGCGCGCCACCTACACACCCTCTACGCCCAATGAATCCGAACAACGCTTGAGACCTCTGTATTACCGCGGCTGCTGGCACAGAGTTAGCCGTCTCTTCCTCTTCTGGTACTATCA


GenBank Integer ID 28435712

GenBank Accession Number AY192335.1

GenBank Defintion Uncultured Verrucomicrobia bacterium clone W3-2F 16S ribosomal RNA gene, partial sequence

This sample shows the additional GenBank fields populated.

amo database query interfaces february 1, 2006

Documents