FAQ
From PTAGISWiki
Top 10 Frequently Asked Questions
How can I tell if a PIT-tagged fish was transported from GRJ, GOJ, LMJ, or MCJ?
You can determine where a PIT-tagged fish was last seen as it passed through a PTAGIS interrogation site by building and running an Interrogation Summary query and then inspecting the value returned in the last monitor name column. At the four smolt transportation sites operated by the Corps of Engineers (GRJ, GOJ, LMJ, and MCJ), a PIT-tagged fish last seen at a monitor with the word "Raceway" or "Sample" in it is generally transported from the facility if the detection occurred during the transportation season.
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How can I remove duplicates from a list of PIT tag codes?
If you are logged in to the PTAGIS Web Portal (http://www.ptagis.org/ptagis), you can register your list of tag codes. Once the list is registered, you can use the Filter Duplicates function on the My Registered Tags page to generate a new list of unique tags.
If you create an Interrogation Summary report with the 'PTAGIS Query Builder', it's possible that the report output will contain multiple records for a single tag detected at two or more interrogation sites. If you want a count of the unique tags in the report, you can capture the tag codes to a registered tag list, and then filter out the duplicates.
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How do I cite PTAGIS, and its database, in a report or peer-reviewed article?
While there does not appear to be an established convention to reference the entirety of data collected in an online database, we suggest the recommendations in the Chicago Manual of Style's citation guide. The year provided in the citation denotes the most recent access to, or retrieval of data from, the database. The form shown in the first example also appears in recent journal articles published by the American Fisheries Society.
- PTAGIS (Columbia Basin PIT Tag Information System). 2008. Pacific States Marine Fisheries Commission, Portland, Oregon. Available: www.ptagis.org. (June 2008).
or
- PTAGIS. The Columbia Basin PIT Tag Information System. Available: www.ptagis.org (accessed June 2008).
It may be more expedient to cite PTAGIS directly within the text, as recommended in Section 8.39 (Software) of the American Fisheries Society's Style Guide, e.g.,
- ... using data obtained from the Columbia Basin PIT Tag Information System (PTAGIS) database (managed by the Pacific States Marine Fisheries Commission; available at http://www.ptagis.org).
How do I request use of the SbyC process?
The PIT Tag Separation by Code (SbyC) process allows researchers to collect or divert specific PIT-tagged fish at certain sites in the mainstem Columbia and Snake rivers. The request and coordination process is documented in the Support > SbyC section of the PTAGIS Web Portal at http://www.ptagis.org/ptagis.
What is a "Duplicate" Tag?
If a tag data file contains a tagging/release record for a PIT tag that has been previously reported as tagged and released in another data file, then the second occurrence of that tag is identified by PTAGIS as a Duplicate Tag. The Duplicate Tag event is stored to the tag_dup_data table in the PTAGIS database, separate from the "true" marking and release event stored in the tag_data table. The Duplicate Tag event is hidden from reports that correlate the original marking and release event data with subsequent recapture, automated detection (interrogation), and mortality events.
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What is an "ORPHAN" Tag?
A PIT tag is categorized as an ORPHAN if PTAGIS receives an interrogation record for that tag before we receive a corresponding tagging record. When PTAGIS receives the actual tagging/release data, the ORPHAN status is automatically updated to reflect the "true" tagging and release properties. Generally, ORPHAN tag records occur when tagged fish are released directly upstream of a PIT tag detection site, and the researcher has not had an opportunity to finalize their marking data and submit those data to PTAGIS. In some instances, a researcher may be unaware that some of his or her tagged fish have not been reported to PTAGIS. In this case, the Tag Distribution and Inventory (TDI) records associated with ORPHAN tags, if available, can be used to alert that researcher to their data omissions.
What is a "DISOWN" record?
A mark/release record with a DISOWN File ID signifies that the PIT tag code was originally reported to PTAGIS in a Tag Data file, but that the tag code was removed from a subsequent version of that Tag Data file.
In 2008, a change was made the Field Data Validation and Loading (FDVL) process to help users detect inadvertent omissions after submitting updated tagging files to PTAGIS. Before the change, when processing a tagging correction, FDVL would delete from the tag_data table any detail record that had been removed from the associated tagging file since its previous submittal. After the change, FDVL now marks each such record with a fictitious file_id of DISOWN, rather than deleting it.
Users may be familiar with another fictitious file_id, ORPHAN, signifying a PIT tag for which one or more interrogation records have been received, but no tagging file has been processed. DISOWN identifies a different sort of anomaly, a tag_data record – for a PIT tag with or without interrogation data – which has been disassociated from tag file header information stored in the database.
ORPHAN and DISOWN records are similar in that either record will be overwritten upon processing a subsequent tagging file that contains the associated PIT tag.
What is a "Test" Tag?
Test tags are PIT tags that are used to verify PIT tag interrogation device operation. Test tags are registered with the PTAGIS database in order to differentiate them from PIT tags used to mark animals. Key chains with embedded PIT tags are registered as test tags.
There are two general types of test tags. The first is a stick tag. The PIT tag is permanently embedded in a rectangular wood dowel about 12 inches long. The stick is passed through the field of a PIT tag antenna to verify system operations. Generally, when stick testing is performed by PTAGIS Field Engineering Technicians, a known number of tags (usually 20) is placed in a fishway or fish flume, and allowed to pass by or pass through an antenna array. The reading efficiency of the detection system can be established using this direct measurement method.
Timer tags are also used to verify system operation. The timer tag is not an actual PIT tag. Rather, it is a device that emits a known PIT tag signal to detection electronics at a pre-programmed interval. This device allows operations and maintenance personnel to see a 'heartbeat' from a detection antenna during extended intervals when tagged fish are absent. Timer tags are also known as fixed reference tags. A Virtual timer tag is not a tag at all, but a specific code generated by a transceiver and routed through the antenna circuitry. In the case of a multiplexing transceiver (MUX), the same virtual timer tag code is routed to all of the active antennas.
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How do I replace the lithium battery in my FS-2001 transceiver?
Instructions to replace the FS-2001 lithium battery can be found at the PTAGIS Web Portal (http://www.ptagis.org/ptagis), on the Documents page of the LIBRARY section. Similar instructions are provided in the September, 2001 PTAGIS Newsletter (Vol. 5, Issue 1), available from the Newsletters page of the LIBRARY section. These instructions and the PTAGIS Newsletter can also be retrieved from the PTAGIS FTP server at ftp://ftp.ptagis.org/Documents/Lithium_Battery_Replacement. Note: Digital Angel now recommends replacing the existing battery with a model CR-2032 or equivalent, rather than the model CR-2016 previously cited.
How do I upgrade the firmware in my FS-2001 transceiver?
FS-2001 transceivers manufactured prior to 2005 generally are not capable of detecting the new generation of Digital Angel PIT tags. These transceivers must have their firmware upgraded in order to decode the new SGL and SST tags now commonly used in the Columbia Basin. All FS-2001 transceivers must be equipped with firmware version 5.0 or higher. The firmware upgrade packages, and upgrade instructions, are available from the Firmware page of the SOFTWARE section of the PTAGIS Web Portal (http://www.ptagis.org/ptagis).
Interrogation Data
Can I reload Interrogation Data files to fix problems with the data?
The short answer is "you can add interrogation records to your existing interrogation data files, but PTAGIS will not recognize changes to records already processed, and will instead process those records as new entries."
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Why do I see detections with identical millisecond timestamps in my MiniMon data files?
The redundant milliseconds happen because the timestamps are assigned by MiniMon, not by the transceiver. Because readers send variable length messages, MiniMon cannot optimize serial I/O on the message length. Instead, it has to rely on hardware interrupts to get data from the serial ports, which are at the mercy of a lot of system related tasks that dictate when they can fire. Therefore MiniMon can process a batch of several tag records in microseconds and assign them all the same millisecond timestamp.
Web Query
Why does my query fail every time I run it, even though it used to work?
There is a bug in our report generator that can cause queries to become partially dropped. If this happens, the query will fail when executed, but still appear in your list of queries. Until we fix the problem, the workaround is to open the query in Query Builder as if you were going to edit it, but skip to the final step and save the query without making any changes. This action re-registers the query and fixes this particular problem.
How do I build a PTAGIS Web Query using the new filter constraints?
The PTAGIS Query Builder application provides access to the millions of mark/release/recovery and automated interrotation event records stored in the PTAGIS database. The business rules for defining required query filters were improved in August, 2006. These changes provide increased flexibility for retrieving records, while simultaneously ensuring that our database constituents do not accidently request more data than they intended.
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How do I build a registered tag list?
Please refer to our recipe for How to make a registered tag list.
How do I get a report of unique fish?
Please refer to How can I remove duplicates from a list of PIT tag codes? above.
When I download the results of a web query into Excel, some columns have leading or trailing zeroes removed. How can I get the real data to show up?
We send web query results in CSV (comma-separated-values) format, which Excel will open and import automatically. This is usually a good thing. But for some RKM values (like 023 or 522.100) or coil IDs (like 09), Excel will automatically make those fields appear as numbers without the leading (or trailing) zeros. To take control of the import process, download our CSV file and replace the file's "csv" extension with a "txt" extension. Then start Excel and import the data file. This will trigger Excel's import wizard and allow you tell Excel what data type each column should be imported as. Import the RKM and/or coil ID columns as text and the leading/trailing zeros will be formatted correctly.
How do I prevent Excel from corrupting my old 400 kHz tag codes?
When directly importing a CSV list that includes PIT tag codes, Excel will corrupt any code consisting entirely of digits except for a single "E". Excel perceives codes with this mask as a value represented in scientific notation, rather than as a hexadecimal value. The solution to this problem is to rename your CSV list with a "TXT" extension; this will force Excel to import all of the tag codes as text. Refer to the article entitled Protecting PIT Tag Data When Importing Files into Excel on page 5 of the July 1998 PTAGIS Newsletter (Vol. 3, Issue 3).
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When I try to change a filter in the query builder, instead of getting a pop-up window asking me to specify the filter, I get logged out.
This could either be a problem with exhausting available memory in your computer or your browser presenting stale credentials. When the problem occurs, check to see how much memory is available. If you don't have enough memory to open one more window, then try closing other applications to see if that helps.
If the problem is not memory-related then you should try clearing the browser cache and restarting the browser.
Some reports fail with the error 'RepletException, not found'.
I am receiving an error message most of the time that I attempt to enter hexadecimal tag data into the complete tag history tool. The following is the message I receive when I submit a data request:
Interactive Reports/New Complete Tag History.11998271313101@local could not be generated for the following reason: inetsoft.sree.RepletException: Replet Interactive Reports/New Complete Tag History.11998271313101@local not found
One of the other computers here does not have this problem.
This kind of problem may be caused by a session time out or a corrupt browser cache of your PTAGIS credentials. Either of those problems should be solved by logging out or logging in, depending on whether or not you are currently logged in. If that doesn't solve the problem, you may want to try to clear your browser's cache or restart your browser.
The queries in "My Queries" are not mine.
Your browser is probably presenting stale credentials. Try clearing your cache and restarting your browser.
How do I clear the cache in Internet Explorer?
The default configuration for Internet Explorer may cause problems when using the PTAGIS web site. We've found it helpful to tell IE to be more aggressive about clearing the cache and not holding on to old credentials. This has fixed problems for people who see the wrong queries in their "My Queries" section or are unable to change or create queries.
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How can I tell how much memory is available to my browser?
If you are running Windows, you can open up the Task Manager and watch the performance tab to see the page file usage and page file usage history graph. (Task Manager can be started in Windows XP by clicking the Start button, selecting run, and entering "taskmgr.exe") Task manager also displays kernel and physical memory. If available or nonpaged memory approaches zero, the web browser will be unable to open new windows.
Can I edit a query after it is submitted but before it is run?
I have a basic question about how the queries are functioning in PTAGIS. When a query is written and ran, does the server save the query parameters and then run the query, or does it fetch them from the saved query when it runs the query? I plan to edit three different queries today to get data from 2001 to 2006. Currently I am letting a query finish running before I edit it for the next year. If I know the query is saving the parameters each time it’s run I can get done quicker and download the reports later.
Answer:
Yes, you can edit a query immediately after submitting it for a run. Your edits will not affect the run of the original query. Whenever you edit a query, you are creating a new version of it. The version number of the query is visible in the name of the completed report, immediately before the ".csv" part of the name.
If you think you might use these queries later, you could make copies of the original query and make your edits to the copies. On the My Queries page, there is a Copy button for this purpose.
I was locked out of PTAGIS for too many incorrect login attempts. How long until I can be permitted to enter the correct password?
Our policy is to lock an account for 30 minutes after 5 incorrect login attempts within 5 minutes.
Why can't I delete a registered tag list? It just says "Failed to delete tag group" when I try.
Try using the method described here: Deleting registered tag lists
Data Anomalies
What is an "ORPHAN" Tag?
A PIT tag is categorized as an ORPHAN if PTAGIS receives an interrogation record for that tag before we receive a corresponding tagging record. When PTAGIS receives the actual tagging/release data, the ORPHAN status is automatically updated to reflect the "true" tagging and release properties. Generally, ORPHAN tag records occur when tagged fish are released directly upstream of a PIT tag detection site, and the researcher has not had an opportunity to finalize their marking data and submit those data to PTAGIS. In some instances, a researcher may be unaware that some of his or her tagged fish have not been reported to PTAGIS. In this case, the Tag Distribution and Inventory (TDI) records associated with ORPHAN tags, if available, can be used to alert that researcher to their data omissions.
What is a "DISOWN" record?
A mark/release record with a DISOWN File ID signifies that the PIT tag code was originally reported to PTAGIS in a Tag Data file, but that the tag code was removed from a subsequent version of that Tag Data file.
A change has been made to FDVL, the Field Data Validation and Loading process, to help users detect inadvertent omissions after submitting updated tagging files to PTAGIS. Before the change, when processing a tagging correction, FDVL would delete from the tag_data table any detail record that had been removed from the associated tagging file since its previous submittal. After the change, FDVL will mark each such record with a fictitious file_id of DISOWN, rather than deleting it.
Users may be familiar with another fictitious file_id, ORPHAN, signifying a PIT tag for which one or more interrogation records have been received, but no tagging file has been processed. DISOWN identifies a different sort of anomaly, a tag_data record – for a PIT tag with or without interrogation data – which has been disassociated from tag file header information stored in the database.
ORPHAN and DISOWN records are similar in that either record will be overwritten upon processing a subsequent tagging file that contains the associated PIT tag.
What is a "Duplicate" Tag?
If a tag data file contains a tagging/release record for a PIT tag that has been previously reported as tagged and released in another data file, then the second occurrence of that tag is identified by PTAGIS as a Duplicate Tag. The Duplicate Tag event is stored to the tag_dup_data table in the PTAGIS database, separate from the "true" marking and release event stored in the tag_data table. The Duplicate Tag event is hidden from reports that correlate the original marking and release event data with subsequent recapture, automated detection (interrogation), and mortality events.
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Transceiver Hardware
How do I replace the lithium battery in my FS-2001 transceiver?
Instructions to replace the FS-2001 lithium battery can be found at the PTAGIS Web Portal (http://www.ptagis.org/ptagis), on the Documents page of the LIBRARY section. Similar instructions are provided in the September, 2001 PTAGIS Newsletter (Vol. 5, Issue 1), available from the Newsletters page of the LIBRARY section. These instructions and the PTAGIS Newsletter can also be retrieved from the PTAGIS FTP server at ftp://ftp.ptagis.org/Documents/Lithium_Battery_Replacement. Note: Digital Angel now recommends replacing the existing battery with a model CR-2032 or equivalent, rather than the model CR-2016 previously cited.
How do I upgrade the firmware in my FS-2001 transceiver?
FS-2001 transceivers manufactured prior to 2005 generally are not capable of detecting the new generation of Digital Angel PIT tags. These transceivers must have their firmware upgraded in order to decode the new SGL and SST tags now commonly used in the Columbia Basin. All FS-2001 transceivers must be equipped with firmware version 5.0 or higher. The firmware upgrade packages, and upgrade instructions, are available from the Firmware page of the SOFTWARE section of the PTAGIS Web Portal (http://www.ptagis.org/ptagis).
Potpourri
How long is the antenna wire in a PIT tag?
According to the manufacturer, the Destron Fearing model TX1400SST 12mm PIT tag contains about 3 meters (9.8 feet) of copper antenna wire.
How did a PIT tag from a steelhead released from Ringold Hatchery end up in New Zealand?
A PIT tag implanted in a Columbia Basin steelhead released from Ringold hatchery in April, 2005, and subsequently detected at Bonneville Dam in May, 2005, was recovered almost two years later, in April, 2007, from a sooty shearwater chick on a small island in the far south of New Zealand.
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