EML: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362014-07-03T18:11:39ZEcoinformatics Redmine
Redmine Bug #6574 (New): document use of ORCID ids in userId fieldhttps://projects.ecoinformatics.org/ecoinfo/issues/65742014-07-03T18:11:39ZMatt Jonesjones@nceas.ucsb.edu
<p>Kyle Braak [GBIF] has requested that we document how to use ORCID ids in EML documentation. He writes:</p>
<blockquote>
<p>Just a thought, but to promote ORCIDs a bit, how about adding <a class="external" href="http://orcid.org/">http://orcid.org/</a> to the list of examples in the "directory" documentation: <a class="external" href="https://knb.ecoinformatics.org/#external//emlparser/docs/eml-2.1.1/./eml-party.html#directory">https://knb.ecoinformatics.org/#external//emlparser/docs/eml-2.1.1/./eml-party.html#directory</a>? Another candidate could be Researcher IDs (e.g. <a class="external" href="http://www.researcherid.com/rid/C-4862-2011">http://www.researcherid.com/rid/C-4862-2011</a>).</p>
</blockquote>
<p>This includes describing the use of the <a class="external" href="http://orcid.org">http://orcid.org</a> site as the directory, and showing an example of an ORCID in the text. We should also mak eit clear that a userId from a public source like ORCID is much more useful than a local userid from a site-specific system.</p> Feature #6283 (New): add field to reference data usage citationshttps://projects.ecoinformatics.org/ecoinfo/issues/62832013-12-06T15:51:34ZMatt Jonesjones@nceas.ucsb.edu
<p>Consider adding an optional top level field to eml-dataset to provide this, possibly something like:</p>
<p><code>/eml/dataset/dataUsageCitation which would be of type CitationType<br /></code></p>
<p>See discussion on eml-dev regarding this issue:<br /> <a class="external" href="http://lists.nceas.ucsb.edu/ecoinformatics/pipermail/eml-dev/2013-December/002004.html">http://lists.nceas.ucsb.edu/ecoinformatics/pipermail/eml-dev/2013-December/002004.html</a></p> Feature #5998 (New): Add publication date property to keywordSethttps://projects.ecoinformatics.org/ecoinfo/issues/59982013-06-06T17:53:02Zben leinfelderleinfelder@nceas.ucsb.edu
<p>From Éamonn Ó Tuama [GBIF] <<a class="email" href="mailto:eotuama@gbif.org">eotuama@gbif.org</a>>:<br />---------<br />Both EML and ISO19115 provide fields for keywords and the name/title of associated thesaurus. However, if the thesaurus name is provided, in the case, of ISO19115, a publication date must also be included. In order to ensure maximum information transfer in cross walks from EML to the new North American Profile of ISO19115 [1], consider adding a conditional date (and date type) property to the EML keywordSet. See example in [2].</p>
<p>[1] <a class="external" href="http://nap.geogratis.gc.ca/metadata/napMetadata-eng.html">http://nap.geogratis.gc.ca/metadata/napMetadata-eng.html</a><br />[2] <a class="external" href="http://nap.geogratis.gc.ca/metadata/examples/napEx1.xml">http://nap.geogratis.gc.ca/metadata/examples/napEx1.xml</a></p> Bug #4939 (New): buildDocBook.xsl missing from release distributionhttps://projects.ecoinformatics.org/ecoinfo/issues/49392010-04-15T22:41:40ZMatt Jonesjones@nceas.ucsb.edu
<p>Gallagher reports:</p>
<p>Anyway, the file buildDocBook.xsl is missing from the tar.gz dist of eml<br />2.1.0. This shows when the clean target is run because that target<br />erases the docs. The docs target requires the xsl...</p> Bug #1991 (In Progress): add fields for information about metadata maintenancehttps://projects.ecoinformatics.org/ecoinfo/issues/19912005-02-28T21:06:24ZMatt Jonesjones@nceas.ucsb.edu
<p>This is a request for additional fields regarding metadata maintenance that I am<br />filing for Xiaoping Wang.</p>
<p>----- Original request from Xiaoping Wang -----------<br />Dear eml-dev:</p>
<p>As mentioned in my email to Matt and Peter (see below), providing necessary<br />timestamp inforamtion for the EML metadata document is important not only to<br />metadata generators but also to metadata users. Both<br />/eml/dataset/maintenance/description and<br />/eml/dataset/maintenance/maintenanceUpdateFrequency in EML schemas are used for<br />description of dataset, not for the metadata document itself. Although we can<br />use /eml/additionalMetadata to say something about the metadata document, I<br />believe that the timestamp information about the EML metadata document is so<br />important that it needs to be highlighted. The following is my recommendataion<br />about the way you can provide more information about the metadata itself.</p>
<p>In the /eml/dataset/res:ResourceGroup, instead of using metadataProvider as one<br />of the elements, use metadataInformation as suggested below:<br /><metadataInformation><br /> A sequency of<br /> <metadataProvider> required (comment: inforamtion<br />about metadata providers is listed here)<br /> <metadataCreationDate> required (comment: the date when<br />the metadata document is originally created)<br /> <metadateMaintenance> Optional (comment: this element is<br />used when the metadata document needs to be updated in the future)<br /> A sequency of<br /> <lastUpdateDate> required (comment: the date of last<br />metadata update)<br /> <oldVule> required (comment: for example, the<br />endDate for rangeOfDates, numberOfRecords for an entity (table), size of entity<br />(table)........ These values will be changed after new data are loaded into the<br />dataset)<br /> <updateFrequence> required (comment: by comapring<br />updateFrequency and lastUpdateDate, metadata developers know when they need to<br />update their metadata document, and metadata users know if the metadata document<br />describes the most current information about the dataset)</p>
<p>These are the necessary elements that I think they should be provided in EML<br />metadata document. Hope my recommendation helps.</p>
<p>Thank you very much for your support.</p>
<p>Xiaoping Wang<br />PMEL /NOAA</p>
<p>---------- End request ----------<br />The full email thread regarding this request can be seen in the EML-dev email<br />archive here:<br /><a class="external" href="http://www.ecoinformatics.org/pipermail/eml-dev/2005-February/001076.html">http://www.ecoinformatics.org/pipermail/eml-dev/2005-February/001076.html</a></p> Bug #1794 (In Progress): modify temporalCoverage to support ongoing data sourceshttps://projects.ecoinformatics.org/ecoinfo/issues/17942004-12-02T01:41:41ZMatt Jonesjones@nceas.ucsb.edu
<p>---- Posted on behalf of Barbara Benson (<a class="email" href="mailto:bjbenson@wisc.edu">bjbenson@wisc.edu</a>) ----</p>
<p>I would like to raise some concerns that have arisen while developing EML<br />documents for the North Temperate Lakes LTER.</p>
<p>Our data reside in an Oracle database, and tables are updated with new data at<br />frequencies ranging from hourly to annually. We are creating EML documents to<br />describe these data, and the data can be accessed dynamically from our website.<br /> Data from instrumented buoys are uploaded to the database every hour and are<br />thus accessible from our website current to within the last hour. Our problem<br />comes from trying to create temporal coverage for the NTL data. In order to<br />have valid EML, it would seem like our options are:</p>
<p>1) to inaccurately describe the end date of a data set by choosing a static<br />date; for example, the EML Best Practices document suggests using the end of the<br />current year<br />2) to choose not to populate temporal coverage, thus having data sets that<br />won't be located by temporal searches<br />3) to create data sets outside our database that are static<br />4) to use the "kluge" solution from a previous draft of the EML Best Practices<br />using the alternative time scale as "ongoing" and leaving the end date blank.</p>
<p>For data sets that are only updated annually, we are willing to create an end<br />date and just change that end date each year in the metadata. We have not<br />decided how to handle temporal coverage for data that are updated more<br />frequently but none of the currently available (valid) options seems desirable.</p>
<p>The current focus for creation of EML documents is to harvest them to the<br />Metacat at the LTER Network Office. The rationale for this harvest is to<br />support the data discovery functionality through Metacat across the LTER<br />datasets. Given the well developed functionality of the NTL dynamic database<br />access and the capability of capturing information about users accessing the NTL<br />data, we want the EML documents to point to our dynamic database access system<br />for each data set. Therefore, we don't find the creation of a static dataset a<br />viable option at the present time when our higher level of functionality is not<br />available centrally and not likely to become available in the near future.</p>
<p>To me the problems with creating temporal coverage for an ongoing data set<br />highlight what I perceive to be a more general problem regarding the<br />conceptualization of what objects EML is designed to describe. The set of<br />objects needs to be bigger than static data sets. There are other data sources<br />that need metadata description, e.g., database tables that are frequently<br />updated, data streams from sensor networks. Some features of the current<br />version of EML seem to be limited by this "static dataset" paradigm. It isn't<br />hard to envision applications for EML attached to data streams.</p>
<p>We would appreciate your response to these issues. We think the next version of<br />EML should accommodate ongoing data sets and allow the end date to be blank.</p>
<p>thanks<br />Barbara Benson</p> Bug #1662 (In Progress): id key definitions in EMLhttps://projects.ecoinformatics.org/ecoinfo/issues/16622004-08-27T00:24:56ZPeter McCartneypeter.mccartney@asu.edu
<p>there are several problems emerging with the unique key definitions in eml. in<br />eml.xsd, there is a key definition that requires all instances of the @id<br />attribute to be unique within the document. when content is to be duplicated<br />there is to be one instance of the content with an id assigned and all other<br />instances are to use the <references> tag to point to that id. id's in a<br />document may be declared as document or system scope, meaning that they are<br />declared to be unique only within the document or within a broader naming<br />authority that is identified in the @system attribute.</p>
<p>Here are some of the problems:<br />1. there no enforced unique constraint on the @system attribute, although it is<br />implicit. Thus it is possible to create a dataset element usint an id with<br />system=cesdataset and a creator with system=asupersonnel. when those systems<br />have each assigned a similar value, you get conflicts. to avoid them, users are<br />forced to change identifiers and break the pointers back to the original source<br />of the content.</p>
<p>2. the spirit of the id and references tags was to insert some degree of<br />normalization that xml inherently lacks. however, it can be a rather arbitrary<br />choice with in the document which instance is the one that gets the content and<br />which ones get the reference pointer. This makes it very difficult for people<br />trying to write tools to edit eml documents since one could easily drop an<br />element that contains elements that contain content that other elements are<br />pointing to. This gratuitously complicates programming for EML and is likely to<br />discourage potential contributors of tools for working with the standard.</p>
<p>3. EML method allows you to embed the eml of related datasets that were used to<br />produce the current one in the methods discussion. conflicts can arise between<br />the identifiers of the embedded datasets. attemping to resolve conflicts between<br />documents using references could mean you have to edit those documents rather<br />than embed them.</p> Bug #1634 (New): units not in eml-unitDictionaryhttps://projects.ecoinformatics.org/ecoinfo/issues/16342004-07-10T00:44:32ZMargaret O'Brienmob@msi.ucsb.edu
<p>As requested, here is the list of customUnits used by sbclter (to date). The<br />current version of this list can be found at the url above. Several of these<br />units need addional attributes or definition. These are commonly-used units in <br />oceanography and limnology.</p>
<p><unit id="reciprocalMeter" name="reciprocalMeter" unitType="lengthReciprocal" <br />abbreviation="m-1" parentSI="meter" multiplerToSI="1"><br /><description>per meter, describes optical properties</description><br /></unit><br /><del><br /><unit id="reciprocalMetersPerSteradian" name="reciprocalMetersPerSteradian" <br />unitType="lengthReciprocal" abbreviation="m-1*sr-1" parentSI="meter" <br />multiplerToSI=""><br /><description>describes directional optical measurements</description><br /></unit><br /></del><br /><unit id="microwattsPerSquareCentimeterPerNanometer" <br />name="microwattsPerSquareCentimeterPerNanometer" unitType="power" parentSI="joule"><br /><description>irradance unit</description><br /></unit><br /><del><br /><unit id="microwattsPerSquareCentimeterPerNanometerPerSteradian" <br />name="microwattsPerSquareCentimeterPerNanometerPerSteradian" unitType="power" <br />parentSI="joule"><br /><description>directional irradiance unit</description><br /></unit><br /></del><br /><unit id="microeinsteinsPerSquareMeterPerSecond" <br />name="microeinsteinsPerSquareMeterPerSecond" unitType="energy" parentSI="joule"><br /><description><br />PAR irradiance unit, Seabird 911. 1Ein = energy of 1 mole photons<br /></description><br /></unit><br /><del><br /><unit id="microeinsteinsPerSquareCentimeterPerSecond" <br />name="microeinsteinsPerSquareCentimeterPerSecond" unitType="energy" <br />parentSI="joule"><br /></del><br /><description><br />PAR Scalar irradiance unit. 1Ein = energy of 1 mole photons<br /></description><br /></unit><br /><del><br /><unit id="decibar" name="decibar" unitType="pressure" abbreviation="dbar" <br />parentSI="pascal" multiplerToSI="10,000"><br /><description>pressure, oceanography</description><br /></unit><br /></del><br /><unit id="hectoPascal" name="hectoPascal" unitType="pressure" abbreviation="hPa" <br />parentSI="pascal" multiplerToSI="100"><br /><description><br />SI unit for atmospheric pressure, equivalent in magnitude to millibar<br /></description><br /></unit><br />-<br /><unit id="percent" name="percent" unitType="massPerMass" abbreviation="o/o" <br />parentSI="gramsPerGram" multiplerToSI=".01"><br /><description>parts per hundred</description><br /></unit></p>
<p><unit id="permil" name="permil" unitType="massPerMass" abbreviation="o/oo" <br />parentSI="gramsPerGram"><br /><description><br />parts per thousand relative to a std composition. UC-delta used for isotope<br />enrichment = (Rx / Rs - 1) ·1000. o/oo used for salinity<br /></description><br /></unit><br /><del><br /><unit id="sigma_unit" name="sigma_unit" unitType="massDensity" <br />parentSI="killogramsPerCubicMeter" constantToSI="-1000" multiplerToSI="1"><br /><description>seawater density = kg/m3 -1000</description><br /></unit><br /></del><br /><unit id="millimolesPerCubicMeter" name="millimolesPerCubicMeter" <br />unitType="amountOfSubstanceConcentration" abbreviation="mmol*m-3" <br />parentSI="molesPerCubicMeter" multiplerToSI=".001"><br /><description>concentration unit</description><br /></unit><br /><del><br /><unit id="micromolesPerLiter" name="micromolesPerLiter" <br />unitType="amountOfSubstanceConcentration" parentSI="molesPerCubicMeter" <br />multiplerToSI=".001"><br /><description><br />concentration, same magnitude as micromolar (for a dissolved constituent)<br /></description><br /></unit><br /></del><br /><unit id="microequivalentsPerLiter" name="microequivalentsPerLiter" <br />unitType="amountOfSubstanceConcentration" parentSI="molesPerCubicMeter" <br />multiplerToSI=""><br /><description><br />concentration of charge (on dissolved ions). A single multiplier to SI is not<br />possible, since conversion includes valence of ion.<br /></description><br /></unit><br /><del><br /><unit id="siemensPerMeter" name="siemensPerMeter" unitType="conductance" <br />abbreviation="S*m-1" parentSI="siemen" multiplerToSI="1"><br /><description>conductivity unit, seawater</description><br /></unit><br /></del><br /><unit id="microsiemensPerCentimeter" name="microsiemensPerCentimeter" <br />unitType="conductance" parentSI="siemen" multiplerToSI=".0001"><br /><description>conductivity unit, freshwater</description><br /></unit><br /><del><br /><unit id="milligramsPerSquareMeterPerDay" name="milligramsPerSquareMeterPerDay" <br />unitType="areaMassDensityRate" abbreviation="mg*m-2*d-1" <br />parentSI="kilogramsPerSquareMeterPerSecond" multiplerToSI="8.64E10"><br /><description><br />areal primary production rate, often in mg-Carbon for an integrated water column<br /></description><br /></unit><br /></del><br /><unit id="kilogramsPerSquareMeterPerDay" name="kilogramsPerSquareMeterPerDay" <br />unitType="areaMassDensityRate" abbreviation="kg*m-2*d-1" <br />parentSI="kilogramsPerSquareMeterPerSecond" multiplerToSI="86400"><br /><description><br />areal primary production rate, may be kg-DW, <del>Carbon or -nitrogen for kelp<br /></description><br /></unit><br /></del><br /><unit id="milligramsPerCubicMeterPerDay" name="milligramsPerCubicMeterPerDay" <br />unitType="volumetricMassDensityRate" abbreviation="mg*m-3*d-1" parentSI="" <br />multiplerToSI=""><br /><description><br />volumetric primary production rate, in a parcel of water<br /></description><br /></unit></p> Bug #1605 (In Progress): missing or erroneous SI units in unitDictionaryhttps://projects.ecoinformatics.org/ecoinfo/issues/16052004-06-16T16:36:53ZMargaret O'Brienmob@msi.ucsb.edu
<p>1. The SI-derived unit "steradian" (sr) appears to be missing. it describes a<br />solid angle, and is the 3-dimensional equivalent of "radian". I dont believe it<br />can be described in terms of any other unit.</p>
<p>2. the "waveNumber" unit is more correctly called reciprocalMeter (m-1), and<br />waveNumber is one of the measurements expressed by this unit (ie, waveNumber=the<br />number of wave cycles in 1 meter). Other measurements which are expressed in m-1<br />include absorbance, scattering and transmittance.</p>
<p>3. the unit "kilogramPerCubicMeter" is named inconsistently. It seems that it<br />should be plural, ie kilogramsPerCubicMeter. This is consistent with other unit<br />names (milligramsPerCubicMeter) and also how it is referenced as a ParentSI<br />attribute.</p> Bug #1000 (In Progress): units missing from Unit Dictionaryhttps://projects.ecoinformatics.org/ecoinfo/issues/10002003-02-21T15:08:39ZMatt Jonesjones@nceas.ucsb.edu
<p>The following exellent email from Don Henshaw addresses a large number of<br />missing or problematic units in the unit dictionary. We need to 1) fix these<br />and others that are identified, and 2) figure out how to release new versions of<br />the eml-unitdictionary without releasing new versions of EML.</p>
<p>---------------- Message from Don Henshaw ---------------------<br />David,<br />I have reviewed the Andrews unit dictionary. The following are units of<br />measurement that we have used at the Andrews that I did not find in<br />eml-2.0.0\eml-unitDictionary.xml, as well as a few other notes.</p>
<p>Thanks,<br />don</p>
<p>pressure: hectopascal (=100 pascals)<br />volume: cubic centimeters<br />volumetricArea: cubic meters per hectare <br />volumetricArea: cubic meters per square meter<br />massDensity: megagrams per cubic meter<br />arealMassDensity: grams per square centimeter<br />arealMassDensity: megagrams per hectare<br />arealMassDensityRate: grams per square meter per day<br />amountOfSubstanceWeight: micromoles per gram<br />amountOfSubstanceWeightFlux: micromoles per gram per day<br />amountOfSubstanceWeightFlux: micromoles per gram per hour<br />amountOfSubstanceWeightFlux: nanomoles per gram per day<br />amountOfSubstanceWeightFlux: nanomoles per gram per hour<br />speed: inches per hour (used more as a rate than a speed)<br />energy?: megajoule per square meter per day (solar radiation)<br />energy?: langley (1 langley=4.187joules per square centimeter, 41870 joules per<br />square meter)<br />energy?: langleys per day (solar radiation)<br />conductance?: micro mhos per centimeter</p>
<p>I do not think there are unit types for the following (I assigned unit type names):<br />massPerMassRate: micrograms per gram per day<br />massPerMassRate: micrograms per gram per hour<br />massPerMassRate: micrograms per gram per week<br />massPerMassRate: nanograms per gram per hour<br />areaPerArea: square meters per hectare<br />luminanceRate??: micromoles per square meter per second (light measurement from<br />LICOR instrument)</p>
<p>Not sure how these fit:<br />milliequivalents per 100 grams<br />pH units<br />ppm (parts per million)<br />ppb (parts per billion)</p>
<p>What about the following use of degrees, minutes, seconds?<br />degrees azimuth<br />decimal degrees of latitude or longitude<br />degrees, minutes, seconds of latitude, longitude</p>
<p>On another topic:<br />Can a julian date be represented in the format string for measurementScale of<br />datetime i.e., YYYYddd</p>
<p>Other notes (being rather picky): pertaining to eml-unitDictionary.xml (2.0.0)<br />following units seems to show wrong abbreviation and multiplier<br />milliGramsPerMilliLiter<br />cubicMicrometersPerGram</p>
<p>The following unit names seem contrary to the convention of showing units in<br />singular form:<br />squareCentimeters<br />squareMillimeters<br />squareKilometers<br />cubicMeterPerKilogram</p>
<p>Not all units show an abbreviation, even when an obvious one exists, ie., kg/ha<br />or g/g liter shows "L" as the abbreviation</p>