Ecoinformatics Redmine: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362016-11-21T19:04:52ZEcoinformatics Redmine
Redmine MetacatUI - Story #7159 (New): Add provenance editor to the Metadata Viewhttps://projects.ecoinformatics.org/ecoinfo/issues/71592016-11-21T19:04:52ZLauren Walkerwalker@nceas.ucsb.eduMetacatUI - Story #7137 (New): Create a data package from scratchhttps://projects.ecoinformatics.org/ecoinfo/issues/71372016-09-30T21:43:56ZLauren Walkerwalker@nceas.ucsb.edu
<p>Serialize an EML document and its system metdata<br />Serialize a resource map and its system metadata<br />Serialize system metadata for the data objects<br />Upload all to the member node</p> MetacatUI - Story #7136 (New): Add a new data file to a packagehttps://projects.ecoinformatics.org/ecoinfo/issues/71362016-09-30T21:42:42ZLauren Walkerwalker@nceas.ucsb.edu
<p>Create a new DataONEObject model<br />Add it to the DataPackage collection<br />On save, upload a new DataONE data object to the member node</p> MetacatUI - Story #7131 (New): Allow users to edit or create data packages in the editorhttps://projects.ecoinformatics.org/ecoinfo/issues/71312016-09-30T21:36:50ZLauren Walkerwalker@nceas.ucsb.eduMetacatUI - Story #7127 (New): Allow editing of EML displayhttps://projects.ecoinformatics.org/ecoinfo/issues/71272016-09-30T21:30:04ZLauren Walkerwalker@nceas.ucsb.eduMetacatUI - Story #7122 (New): Dates sectionhttps://projects.ecoinformatics.org/ecoinfo/issues/71222016-09-30T21:26:48ZLauren Walkerwalker@nceas.ucsb.edu
<p>For now, just a simple begin and end date</p> MetacatUI - Story #7118 (New): Create a new EML and its System Meta doc on a member nodehttps://projects.ecoinformatics.org/ecoinfo/issues/71182016-09-30T21:22:44ZLauren Walkerwalker@nceas.ucsb.eduMetacatUI - Story #7040 (In Progress): A client side data and metadata manager and editorhttps://projects.ecoinformatics.org/ecoinfo/issues/70402016-07-06T21:32:54ZChris Jonescjones@nceas.ucsb.edu
<p>We want to be able to provide basic metadata management and data upload for researchers using a client-side app that is a replacement for the Metacat Data Registry (server-side Perl script.) This ticket is the container story for this work. We need to develop requirements, mockups, and use cases to convey the scope of the work before (and possibly during) development. Since this is a major change in both functionality and UI layout, we'll target this for a 2.0.0 release.</p>
<p>For development, we'll be extending the existing Backbone application with new classes that:</p>
<p>1) Support the creation and parsing of DataONE SystemMetadata,</p>
<p>2) Support the creation and parsing of OAI-ORE resource maps</p>
<p>3) Support the creation and parsing of EML science metadata documents</p>
<p>4) Support the future creation and parsing of ISO 19139 science metadata documents</p>
<p>5) Support the future creation and parsing of FGDC CSDGM science metadata documents</p>
<p>Design documents are being developed here: <a class="external" href="https://github.com/NCEAS/metacatui/blob/master/metacatui/docs/design/editor">https://github.com/NCEAS/metacatui/blob/master/metacatui/docs/design/editor</a></p> Community Dynamics Toolbox - Story #6389 (New): create example analysis and workflowshttps://projects.ecoinformatics.org/ecoinfo/issues/63892014-01-16T21:53:46ZMatt Jonesjones@nceas.ucsb.edu
<p>Need to develop example end-to-end for the workshop.</p> Community Dynamics Toolbox - Dataset #6379 (New): Small Mammal Mark-Recapture Population Dynamics...https://projects.ecoinformatics.org/ecoinfo/issues/63792014-01-15T18:35:54ZSydney Jonessyd@sevilleta.unm.edu
<p>This file contains mark/recapture trapping data collected from 1989-2012 on permanently established web trapping arrays at 8 sites on the Sevilleta NWR. At each site 3 trapping webs are sampled for 3 consecutive nights in spring and fall. Not all sites have been trapped for the entire period. Each trapping web consists of 145 rebar stakes numbered from 1-145. There are 148 traps deployed on each web: 12 along each of 12 spokes radiating out from a central point (stake <a class="issue tracker-1 status-3 priority-5 priority-highest closed" title="Bug: revisions to software metadata standard (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/145">#145</a>) plus 4 traps at the center point. The trapping sites are representative of Chihuahuan Desert Grassland, Chihuahuan Desert Shrubland, Pinyon-Juniper Woodland, Juniper Savanna, Plains-Mesa Sand Scrub and Blue Grama Grassland.</p>
<p>Sampling Design<br />Permanent capture-mark-release trapping webs were used to estimate density (number of animals per unit area) of each rodent species at each site. The method makes use of concepts from distance sampling, i.e., point counts or line-intercept techniques. The method makes no attempts to model capture-history data, therefore it was not necessary to follow individuals through time (between sessions). Distance sampling methods allow for sighting or detection (capture) probabilities to decrease with increasing distance from the point or line. The modeling of detection probability as a function of distance forms the basis for estimation. Trapping webs were designed to provide a gradient of capture probabilities, decreasing with distance from the web center. Density estimation from the trapping web was based on three assumptions:1. All animals located at the center of the web were caught with probability 1.0; 2. Individuals did not move preferentially toward or away from the web center; 3. Distances from the web center to each trap station were measured accurately. Each web consisted of 12 trap lines radiating around a center station, each line with 12 permanently-marked trap stations. In order to increase the odds of capturing any animals inhabiting the center of a web, the center station had four traps, each pointing in a cardinal direction, and the first four stations of each trap line were spaced only 5 m apart, providing a trap saturation effect. The remaining eight stations in a trap line were spaced at 10 m intervals. The web thus established a series of concentric rings of traps. Traps in the ring nearest the web center are close together, while the distances separating traps that form a particular ring increase with increasing distance of the ring from the web center. The idea is that the web configuration produces a gradient in trap density and, therefore, in the probability of capture. Three randomly distributed trapping webs were constructed at each site. The perimeters of webs were placed at least 100 m apart in order to minimize homerange overlap for individuals captured in the outer portion of neighboring webs.</p>
<p>Measurement Techniques<br />Each site containing three webs was sampled for three consecutive nights during spring (in mid May or early June) and summer (in mid July or early August for years 1989 to 1993, then mid September to early October for years 1994 through 2000). In that rodent populations were not sampled monthly over the study period, there is no certainly that either spring or summer trapping times actually captured annual population highs or lows. Based on reproductive data in the literature, an assumption was made that sampling times chosen represent periods of the year when rodents have undergone, and would register, significant seasonal change in density. During each trapping session, one Sherman live trap (model XLF15 or SFAL, H. B. Sherman Traps, Tallahassee, FL) was placed, baited with rolled oats, and set at each permanent, numbered station (four in the center) on each web, for a total 444 traps over three webs. Traps were checked at dawn each day, closed during the day, and reset just before dusk. Habitat, trap station number, species, sex, age (adult or juvenile), mass, body measurements (total length, tail length, hind foot length, ear length), and reproductive condition (males: scrotal or non-scrotal; females: lactating, vaginal or pregnant) were recorded for each initial capture of an individual. Each animal was marked on the belly with a permanent ink felt pen in order to distinguish it from other individuals during the same trapping session. The trap station number for an initial capture related to a particular trapping ring on a web and, therefore, to a particular distance from the center of the web. The area sampled by a ring of traps was computed based on circular zones whose limits are defined by points halfway between adjacent traps along trap lines; an additional 25 m radius was added to the outer ring of traps in order to account for homerange size of individuals caught on the outer ring.</p>
<p>Analytical Procedures<br />Area trapped and number of individuals caught for each ring of traps was the basis for estimating the probability density function of the area sampled. The program DISTANCE produced the estimators used to calculate density. Where sample size for a particular species and web was less than an arbitrarily chosen n=10, the number of individuals captured during that session was simply divided into the area of the web plus the additional 25 m radius (4.9087 ha). This dataset includes only the raw capture data.</p> Community Dynamics Toolbox - Dataset #6378 (New): Grassland Vegetation Line-Intercept Transects a...https://projects.ecoinformatics.org/ecoinfo/issues/63782014-01-15T18:31:50ZSydney Jonessyd@sevilleta.unm.edu
<p>In 1989, line-intercept transects were installed to evaluate temporal and spatial dynamics across vegetation transition zones. Currently, a 400m transect is sampled at a grassland site (Deep Well) which is dominated by Bouteloua eriopoda (black grama) and, near the southern end of the transect, B. gracilis (blue grama). A second grassland site (Five Points), dominated by B. eriopoda and, to the south, Larrea tridentata (creosote), is also sampled. Both sites are sampled twice a year, in May/June and September/October, and measurements are taken at a one-centimeter resolution. The biannual sampling protocol detects potential responses in both cool and warm season plants as well as pre- and post-monsoon dynamics. Several transects have been discontinued and data archived within SEV200.</p>
<p>Preparing Transects for Measurement:<br />A 100m measuring tape is unrolled and affixed to permanent pieces of rebar hammered into the ground at each of the four segments of a 400 m transect. For example, a tape is attached to the 0 meter (north) rebar stake and run to the 100 meter (south) stake. The tape is stretched as tightly as possible to get the straightest line. Windy days should be avoided as the wind moves the tape and results in inaccurate data.</p>
<p>Recording data:<br />Crew members work independently, each doing a 100 m segment simultaneously. Microcassette recorders and standard microcassettes are used to record the data. File names should be written on the cassettes as "fp" (Five Points), "dw" (Deep Well), or "dwb" (Deep Well-burn) for the location, followed by the transect number, date, and initials of the recorder. An introductory statement is recorded on the cassette (e.g. "It's May 9, 2099, Joe Smith recording at Deep Well Transect 2." <br />Each species or substrate (i.e., bare soil, litter) that intersects the tape and occupies at least one centimeter is recorded whether rooted beneath the tape or not. Observations are recorded at the cm level, the point at which the species or substrate first crosses the tape being stated. This starting location is noted but the ending point is considered to be the starting point of the next species or substrate. For example, Bouteloua eriopoda encountered at 12m 79cm, litter encountered at 12m 82 cm, bare soil at 12m 85 cm, and so forth.</p> Community Dynamics Toolbox - Dataset #6377 (New): Konza vegetation species composition (1989-2011)https://projects.ecoinformatics.org/ecoinfo/issues/63772014-01-15T18:27:02ZSydney Jonessyd@sevilleta.unm.edu
<p>Canopy coverage and frequency were recorded in 20 circular 10 sq m plots. Six treatments were sampled, three ungrazed and three to grazed by native grazers. In each case one of the three watersheds was unburned, another burned annually in April, the third burned every four years in April. In each treatment two soils were sampled: a lower-slope deep fertile nonrocky soil (tully silty clay loam), and a shallow rocky soil (florence cherty silt loam) on level to gently sloping ridges. In 1983 another ungrazed annual burn area (1c) was added (both tully and florence soils) because original area (1d) appeared aberrant.</p> Community Dynamics Toolbox - Dataset #6376 (New): Konza seasonal summary of numbers of small mamm...https://projects.ecoinformatics.org/ecoinfo/issues/63762014-01-15T18:20:50ZSydney Jonessyd@sevilleta.unm.edu
<p>Data set contains seasonal summaries (spring, summer and fall) of the number of individuals of each species of small mammal caught (relative density) on each grassland census line. Each record contains trapline, year of last fire and number of individuals per species. These live trap records are based on daily captures during three 4-day trapping peroids, March, July and October, for each of 20 permanent census lines established on 10 fire-grazing treatments (2 lines per treatment). These 10 fire-grazing treatments are one unburned, one annual burn and one 4- year burn site to be grazed by native ungulates and one unburned, one annual burn, four 4-year burn and one 10-year burn site not grazed by ungulates.</p> Semtools - Story #6250 (New): Create domain ontology (measurement types)https://projects.ecoinformatics.org/ecoinfo/issues/62502013-11-26T17:14:44Zben leinfelderleinfelder@nceas.ucsb.edu
<p>Will we support many extensions of a core ontology?<br />Based on OBOE?</p> Semtools - Story #6249 (New): Define annotation modelhttps://projects.ecoinformatics.org/ecoinfo/issues/62492013-11-26T17:13:43Zben leinfelderleinfelder@nceas.ucsb.edu