February 1, 2006 Page 1 AMO Database Query Interfaces February 1, 2006 Here are some notes on screen layouts for AMO database queries. Hopefully this document.

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Presentation transcript:

February 1, 2006 Page 1 AMO Database Query Interfaces February 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 Page 2 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 Page 3 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 Page 4 Screen Data: Sequence Query Screen There 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 ( trix_env.asp). trix_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 ( htm ). htm An aspect of MaNIS is the ability to select from a concept list - an open query with a limited set of user options. ( vlet?action=menu&loc=http%3A%2F%2Fbnhm.berkel ey.museum%2Fmanis%2FDwC%2Fdarwin2jrwInfodo. xml&reqType=search) vlet?action=menu&loc=http%3A%2F%2Fbnhm.berkel ey.museum%2Fmanis%2FDwC%2Fdarwin2jrwInfodo. xml&reqType=search 12 Finally there are joint queries that span more than one database. MaNIS uses this (also on manis%2FDwC%2Fdarwin2jrwInfodo.xml&reqType=search ). AMO will want to include this in our interface, though I recommend we develop our single database interface first. manis%2FDwC%2Fdarwin2jrwInfodo.xml&reqType=search 3

February 1, 2006 Page 5 Screen Data: Sequence Query Screen The 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 Sample Date Geochemistry 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 Page 6 Screen Data: Sequence List Screen Location IDLocation NameAMO Sequence Name GenBank Accession # BasesSample IDSample Date location. locationID location.locNamesequence. sequenceName sequence. GenBankNumber sequence. pairs soilsample. soilsampleID soilsample. sampleDate Talus site north probe T3_A_C1AY Talus site north probe T3_A_D1AY Talus site data logger T0-D3AY Talus site data logger T0-D12AY 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 Page 7 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) h Alternative #1 Alternative #2

February 1, 2006 Page 8 Screen Data: Sequence Detail Screen 16s rRNA Gene Sequence for sequence.sequenceName sequence.sequence Format: lay the sequence out in column and row format: each row of base pairs has 6 blocks of 10 See ( for an example of this layout. See next slide for an example sequence. Number of base pairs= sequence.pairs GenBank Integer IDsequence.GenBankGI GenBank Accession Numbersequence.GenBankNumber GenBank Defintionsequence.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 Page 9 Sequence Detail Sample Data 16s rRNA Gene Sequence for T3_A_C1 GCTCACACCGATAGTCCCTCTAAGAAGTCGCGTCCAAAGGAAGAATCCTTTGTCGAACTATTTAGCAGGTCGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCACTC CACCAACTAAGAACGGCCATGCACCACCACCCACAGAATCAAGAAAGATCTTCAATCTGTCAATCCTTACTGTGTCTGGACCTGGTAAGTTTTCCCGTGTTGAGTCAAATTA AGCCGCAGGCTCCACTCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCGAAT GAAGTCGAAAATGCAACGTTCACTCATCCCTAGTCGGCATAGTTTATGGTTGAGACTACGACGGTATCTGATCGTCTTCGATCCCCCAACTTTCGTTCTTGATTAAAGAAGAC ATCCTTGGTGAATGCTTTCGCATAAGTTAGTCTTCAGCGAATCCGAGAATTTCACCTCTGGCCGCTGAATACTAGCACCCCCAACTGTCCCTATCAATCATTACTTCAGTCCT AGAAACCAACAAAATAGAACCGAAGTCCTAAATTATTATTCCATGCTAATGTATTCATAGCATAAAGCCTGCTTGAAACACTCTAA 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 Page 10 Sequence Detail Sample Data 16s rRNA Gene Sequence for T3_A_D1 CTTGAGCCAAAGTCCCTCTAAGAAGCTGGCGACCAACAAAAGTCAATCTAGCTATTTAGCAGGTCANGGTCTCGTTCGTTATCGCAATTAAGCAGACAAATCACTCCACCAA CTAAGAACGGCCATGCACCACCACCCATATAATCAAGAAAGAGCTATCAATCTGTCAATCCTAAACATGTCTGGACCTGGTGAGTTTTCCCGTGTTGAGTCAAATTAAGCCG CAGGCTCCACGCCTTGCGCAATTTCTTAGGCTTGTAGCCTAAAAGCACGATCATATCTTAACGAATTACAATAATTCGACGACCTCCACTTGATCTGTGGACCCTAGAAGGG TTGCAGGTCAGCTATAAATGCCGTCCATGCAGTTAAAAGGTCTAACCGAGCGAATCGGTCATATAGGCACCACAAGAGTGGTTAATCTGGTGCCCTTCCGTCAATTTCTTTA AGTTTCAGCCTTGCGACCATACTCCCCCCAGAGCCCAAAAACTTTGATTTCTCGTAAGGTGCCGAACGGGGCATAAAAAACCACCGTCCGATCCCTAGTCGGCATAGTTTAT GGTTAAGACTACGACGGTATCTGATCGTCTTCGATCCCCTAACTTTCGTTCACTGATTAATGAAAACATCCTTGGCGAATGCTTTCGCAATAGTTAGTC Number of base pairs= 659 GenBank Integer ID(not yet assigned) GenBank Accession Number(not yet assigned) GenBank Defintion(not yet defined) This sample corresponds to line 2 on the “list screen” sample data slide.

February 1, 2006 Page 11 Sequence Detail Sample Data 16s rRNA Gene Sequence for T0-D3 ACACTGCTCTCTATCAGTCTTTGACTGTTACTGTGAGAAAATTAGAGTGTTTCAAAGCAGGCTATTGCAGGAATACATTAGCATGGAATAACGAACGTCTAGAATATTGGTTA ATTCTAGATAACGATTAATAGGGACAGTTGGGGGCATTAGTATTTAATTGTCAGAGGTGAAATTCTTGGATTATTTAAAGACTAACGTATGCGAAAGCATTTGCCAAGGATGT TTTCATTAATCAAGAACGAAAGATAGGGGATCAAAGACGATCAGATACCGTCGTAGTCCTATCTATAAACTATGCCGACTAGGGATTAGGGTGGAAAAGTACCATCTTAGTA CCTTATGAGAAATCAAAGTCTTTGGGTTCTGGGGGGAGTATGGTCGCAAGACTGAAACTTAAAGAAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATT TGACTCAACACGGGGAAACTTACCAGGTCCAGACGTAGTAAGGATTGACAGATTGATAGCTCTTTCTTGATTCTATGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAG TGATTTGTCTGGTTAATTCCGTTAACGAACGAGACCTTAACCTGCTAACTAGACTAGTCCATTTTATGGATTCAGTCTTCTTAGAGGGACTATGTTGCGASAGCACAGGAAGT TTGAGGCAA Number of base pairs= 681 GenBank Integer ID(not yet assigned) GenBank Accession Number(not yet assigned) GenBank Defintion(not yet defined) This sample corresponds to line 3 on the “list screen” sample data slide.

February 1, 2006 Page 12 Sequence Detail Sample Data 16s rRNA Gene Sequence for T0-D3 GTAGTTGGATTTGGATGGGTTGTTGCGGTCCGCTCTGGTGAGTACTGCTGTGGCCTATCTTTCTGCCGGGGACGGGCTCCTGGGCTTCACTGTCCGGGACTGGAGTGGCG ATGTTACTTTGAGTAAATTAGAGTGTTCAAAGCAGGCNTACGCTCTGAATACTTTAGCATGGAATAACACGATAGGACTCTGGCCTATCTTGTTGGTCTGTAGGACCGGAGT AATGATTAAGAGGGACAGTCGGGGGCATTCGTATTTCATTGTCAGAGGTGAAATTCTTGGATTTATGAAAGACGAACTACTGCGAAAGCATTTGCCAAGGATGTTTTCATTA ATCAAGAACGAAAGTTGGGGGCTCGAAGACGATTAGATACCGTNGTAGTCTCAACCATAAACGATGCCGACTAGGGATTGGCGGATGTTTATTCAATGACTCCGCCAGCAC CTTATGAGAAATCAAAGTTTTTGGGTTCCGGGGGGAGTATGGTCGCAAGGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGCGTGGAGCCTGCGGCTTAATTT GACTCAACACGGGAAAACTTACCAGGTCCAGACATAGTGAGGATTGACAGATTGAGAGCTCTTTCTTGATTCTATGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGGTT GCCTTGTCAGGTTGATTCCGGTAACGAACGAGACCTCAGCCTGCTAAATAGTCCTAGTCGCTTCTTGCGGCTAGCTGACTTCTTAGAGGGACTATGGCGTTAGTCAAGGAA GTATGAGTTTGAGGCAA Number of base pairs= 681 GenBank Integer ID(not yet assigned) GenBank Accession Number(not yet assigned) GenBank Defintion(not yet defined) This sample corresponds to line 4 on the “list screen” sample data slide.

February 1, 2006 Page 13 Sequence Detail Sample Data 16s rRNA Gene Sequence for (none) GTGTCTTTCGACACTCGCCGGCTTTCACCGGTTTAGAGATGCATGTCAAGGCCTGGTAAGGTTCTTCGCGTTGCATCGAATTGAGCCACATACTCCACCGCTTGTGCGGGT CCCCGTCAATTTCTTTGAGTTTTAATCTTGCGACCGTACTCCCCAGGCGGCACGTTTAACGCGTTAGCTCCGGCGCAGAAGGGGTCGAATCCCCCCACACCAAACGTGCAC CGTTTACTGCCAGGACTACCGGGGTATCTAATCCCGTTTGCTCCCCTGGCCTTCGTGTCTCAGTGTCAGGAACTGTCCAGAGACCCGCCTTCGCCGCTGGTCTTCCTTACG ATATCTACGCATTTCACTGCTACACCGTAAATTCCAGTCTCCTCTCCAGTCCTCAAGCACGCCAGTATCGAATGCAGTTTCGGAGTTAAGCTCCGAAATTTCACACCCGACTT AGCGCGCCACCTACACACCCTCTACGCCCAATGAATCCGAACAACGCTTGAGACCTCTGTATTACCGCGGCTGCTGGCACAGAGTTAGCCGTCTCTTCCTCTTCTGGTACTA TCA Number of base pairs= 561 GenBank Integer ID GenBank Accession NumberAY GenBank DefintionUncultured Verrucomicrobia bacterium clone W3-2F 16S ribosomal RNA gene, partial sequence This sample shows the additional GenBank fields populated.